diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..8af1409 --- /dev/null +++ b/.gitignore @@ -0,0 +1,4 @@ +# Folder +#========= +backup +/Docs/build diff --git a/Docs/Makefile b/Docs/Makefile new file mode 100644 index 0000000..d0c3cbf --- /dev/null +++ b/Docs/Makefile @@ -0,0 +1,20 @@ +# Minimal makefile for Sphinx documentation +# + +# You can set these variables from the command line, and also +# from the environment for the first two. +SPHINXOPTS ?= +SPHINXBUILD ?= sphinx-build +SOURCEDIR = source +BUILDDIR = build + +# Put it first so that "make" without argument is like "make help". +help: + @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + +.PHONY: help Makefile + +# Catch-all target: route all unknown targets to Sphinx using the new +# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). +%: Makefile + @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/Docs/make.bat b/Docs/make.bat new file mode 100644 index 0000000..6247f7e --- /dev/null +++ b/Docs/make.bat @@ -0,0 +1,35 @@ +@ECHO OFF + +pushd %~dp0 + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set SOURCEDIR=source +set BUILDDIR=build + +if "%1" == "" goto help + +%SPHINXBUILD% >NUL 2>NUL +if errorlevel 9009 ( + echo. + echo.The 'sphinx-build' command was not found. Make sure you have Sphinx + echo.installed, then set the SPHINXBUILD environment variable to point + echo.to the full path of the 'sphinx-build' executable. Alternatively you + echo.may add the Sphinx directory to PATH. + echo. + echo.If you don't have Sphinx installed, grab it from + echo.http://sphinx-doc.org/ + exit /b 1 +) + +%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% +goto end + +:help +%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% + +:end +popd diff --git a/Docs/source/0-setting-up-flos.rst b/Docs/source/0-setting-up-flos.rst new file mode 100644 index 0000000..2382c54 --- /dev/null +++ b/Docs/source/0-setting-up-flos.rst @@ -0,0 +1 @@ +.. include:: ./content/setting-up-flos.rst diff --git a/Docs/source/1-some-basics.rst b/Docs/source/1-some-basics.rst new file mode 100644 index 0000000..670427c --- /dev/null +++ b/Docs/source/1-some-basics.rst @@ -0,0 +1 @@ +.. include:: ./content/basics.rst diff --git a/Docs/source/2-tutorials.rst b/Docs/source/2-tutorials.rst new file mode 100644 index 0000000..41f901f --- /dev/null +++ b/Docs/source/2-tutorials.rst @@ -0,0 +1 @@ +.. include:: ./content/tutorials.rst diff --git a/Docs/source/conf.py b/Docs/source/conf.py new file mode 100644 index 0000000..9ce39d6 --- /dev/null +++ b/Docs/source/conf.py @@ -0,0 +1,55 @@ +# Configuration file for the Sphinx documentation builder. +# +# This file only contains a selection of the most common options. For a full +# list see the documentation: +# https://www.sphinx-doc.org/en/master/usage/configuration.html + +# -- Path setup -------------------------------------------------------------- + +# If extensions (or modules to document with autodoc) are in another directory, +# add these directories to sys.path here. If the directory is relative to the +# documentation root, use os.path.abspath to make it absolute, like shown here. +# +# import os +# import sys +# sys.path.insert(0, os.path.abspath('.')) + + +# -- Project information ----------------------------------------------------- + +project = 'flos-documentation' +copyright = '2020, A.Akhtar' +author = 'A.Akhtar' + +# The full version, including alpha/beta/rc tags +release = '1.0' + + +# -- General configuration --------------------------------------------------- +master_doc = 'index' +# Add any Sphinx extension module names here, as strings. They can be +# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom +# ones. +extensions = [ +] + +# Add any paths that contain templates here, relative to this directory. +templates_path = ['_templates'] + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +# This pattern also affects html_static_path and html_extra_path. +exclude_patterns = [] + + +# -- Options for HTML output ------------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +# +#html_theme = 'alabaster' +html_theme ='default' +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = ['_static'] diff --git a/Docs/source/content/basics.rst b/Docs/source/content/basics.rst new file mode 100644 index 0000000..e2edbf1 --- /dev/null +++ b/Docs/source/content/basics.rst @@ -0,0 +1,630 @@ +Basic of FLOS +============= + + +.. figure:: ./images/2.png + :width: 400px + + Flos Architecture + + +Basics +------ +How it Works?! +.............. + +Imagine you have a program which has 3 distinct places where interaction might occur: :: + + program main + call initialize() + call calculate() + call finalize() + end program + +At each **intermediate point** one wishes to communicate with a scripting language. flook lets you communicate fortran and Lua hence it called Flook=fortran+Lua+hook. + +SIESTA Intermediate Points +.......................... + +When you run SIESTA with FLOOK enabled you have 7 **intermediate point** to communicate: + (1) Right after reading initial options + (2) Right before SCF step starts, but at each MD step + (3) At the start of each SCF step + (4) After each SCF has finished + (5) When moving the atoms, right after the FORCES step + (6) When SIESTA start Analyse (Post-Processing) + (7) When SIESTA is complete, just before it exists + +We call above **intermediate points** state in lua script you could communicate with SIESTA viastate defination like this: :: + + if siesta.state == siesta.INITIALIZE + if siesta.state == siesta.INIT_MD + if siesta.state == siesta.SCF_LOOP + if siesta.state == siesta.FORCES + if siesta.state == siesta.MOVE + if siesta.state == siesta.ANALYSIS + if siesta.state == siesta.FINALIZE + +How to Communicate with SIESTA +.............................. + +For Communicate with siesta with it consist of two step : + +(1) set these input SIESTA flags in fdf file: + * set ``MD.TypeOfRun LUA`` + * set ``LUA.Script {NAME OF YOUR SCRIPT}.lua`` +(2) Provide the script ``{NAME OF YOUR SCRIPT}.lua`` + +.. NOTE:: + + The ``{NAME OF YOUR SCRIPT}.lua`` should be in same folder of ``psf`` & ``fdf`` files. + +How to prepare the LUA script for SIESTA +........................................ + +The SIESTA LUA scripts contains two Parts: + + (1) The Main Siesta Communicator function. + (2) The user defined specific function. + +The Main function contains the **intermediate points** states : :: + + function siesta_comm() + -- Do the actual communication with SIESTA + + if siesta.state == siesta.INITIALIZE then + . + . + . + end + + if siesta.state == siesta.INIT_MD then + . + . + . + end + + if siesta.state == siesta.SCF_LOOP then + . + . + . + end + + if siesta.state == siesta.FORCES then + . + . + . + end + + if siesta.state == siesta.MOVE then + . + . + . + end + + if siesta.state == siesta.ANALYSIS then + . + . + . + end + + if siesta.state == siesta.FINALIZE then + . + . + . + end + end + +in each part of ``siesta.state`` we could either send or receive data with siesta dictionary. we will discuss that in () section. + +The user defined function which is a normal function defined by user for specific task. For instance the above function is counter with a return : :: + + -- Step the cutoff counter and return + -- true if successfull (i.e. if there are + -- any more to check left). + -- This function will also step past values + function step_cutoff(cur_cutoff) + + if icutoff < #cutoff then + icutoff = icutoff + 1 + else + return false + end + + if cutoff[icutoff] <= cur_cutoff then + cutoff[icutoff] = cutoff[icutoff-1] + Etot[icutoff] = Etot[icutoff-1] + return step_cutoff(cur_cutoff) + end + + return true + end + +SIESTA LUA Dictionary +..................... + +In each **intermediate points** states we could send or receive data via special name we call them SIESTA LUA dictionary. Here we categorized them: + + :slabel: + SystemLabel + + :DM_history_depth: + DM.HistoryDepth + + Output Options: + + :dumpcharge: + Write.DenChar + + :mullipop: + Write.MullikenPop + + :hirshpop: + Write.HirshfeldPop + + :voropop: + Write.VoronoiPop + + SCF Options: + + :min_nscf: + SCF.MinIterations + + :nscf: + SCF.MaxIterations + + :mixH: + SCF.MixHamiltonian + + :mix_charge: + SCF.MixCharge + + :maxsav: + SCF.NumberPulay + + :broyden_maxit: + SCF.NumberBroyden + + :wmix: + SCF.MixingWeight + + :nkick: + SCF.NumberKick + + :wmixkick: + SCF.KickMixingWeight + + SCF Mixing Options (NEW): + + :scf_mixs(1)%w: + SCF.Mixer.Weight + + :scf_mixs(1)%restart: + SCF.Mixer.Restart + + :scf_mixs(1)%n_itt: + SCF.Mixer.Iterations + + :monitor_forces_in_scf: + SCF.MonitorForces + + :temp: + electronicTemperature + + SCF Convergence Criteria: + + :converge_Eharr: + SCF.Harris.Converge + + :tolerance_Eharr: + SCF.Harris.Tolerance + + :converge_DM: + SCF.DM.Converge + + :dDtol: + SCF.DM.Tolerance + + :converge_EDM: + SCF.EDM.Converge + + :tolerance_EDM: + SCF.EDM.Tolerance + + :converge_H: + SCF.H.Converge + + :dHtol: + SCF.H.Tolerance + + :converge_FreeE: + SCF.FreeE.Converge + + :tolerance_FreeE: + SCF.FreeE.Tolerance + + :dxmax: + MD.MaxDispl + + :ftol: + MD.MaxForceTol + + :strtol: + MD.MaxStressTol + + :ifinal: + MD.FinalTimeStep + + :dx: + MD.FC.Displ + + :ia1: + MD.FC.First + + :ia2: + MD.FC.Last + + :tt: + MD.Temperature.Target + + :RelaxCellOnly: + MD.Relax.CellOnly + + :varcel: + MD.Relax.Cell + + :inicoor: + MD.Steps.First + + :fincoor: + MD.Steps.Last + + :DM_history_depth: + MD.DM.History.Depth + + Write Options: + + :saveHS: + Write.HS + + :writeDM: + Write.DM + + :write_DM_at_end_of_cycle: + Write.EndOfCycle.DM + + :writeH: + Write.H + + :write_H_at_end_of_cycle: + Write.EndOfCycle.H + + :writeF: + Write.Forces + + :UseSaveDM: + Use.DM + + :hirshpop: + Write.Hirshfeld + + :voropop: + Write.Voronoi + + Mesh Options: + + :g2cut: + Mesh.Cutoff.Minimum + + :saverho: + Mesh.Write.Rho + + :savedrho: + Mesh.Write.DeltaRho + + :saverhoxc: + Mesh.Write.RhoXC + + :savevh: + Mesh.Write.HartreePotential + + :savevna: + Mesh.Write.NeutralAtomPotential + + :savevt: + Mesh.Write.TotalPotential + + :savepsch: + Mesh.Write.IonicRho + + :savebader: + Mesh.Write.BaderRho + + :savetoch: + Mesh.Write.TotalRho + + Geometry Options: + + :na_u: + geom.na_u + + :ucell: + geom.cell + + :ucell_last: + geom.cell_last + + :vcell: + geom.vcell + + :nsc: + geom.nsc + + :r2: + geom.xa + + :r2: + geom.xa_last + + :va: + geom.va + + Species Options: + + :isa(1:na_u): + geom.species + + :iza(1:na_u): + geom.z + + :lasto(1:na_u): + geom.last_orbital + + :amass: + geom.mass + + :qa(1:na_u): + geom.neutral_charge + + :Datm(1:no_u): + geom.orbital_charge + + Force & Stress Options + + :cfa: + geom.fa + + :fa: + geom.fa_pristine + + :cfa: + geom.fa_constrained + + :cstress: + geom.stress + + :stress: + geom.stress_pristine + + :cstress: + geom.stress_constrained + + + Energies + + :DEna: + E.neutral_atom + + :DUscf: + E.electrostatic + + :Ef: + E.fermi + + :Eharrs: + E.harris + + :Ekin: + E.kinetic + + :Etot: + E.total + + :Exc: + E.exchange_correlation + + :FreeE: + E.free + + :Ekinion: + E.ions_kinetic + + :Eions: + E.ions + + :Ebs: + E.band_structure + + :Eso: + E.spin_orbit + + :Eldau: + E.ldau + + :NEGF_DE: + E.negf.dN + + :NEGF_Eharrs: + E.negf.harris + + :NEGF_Etot: + E.negf.total + + :NEGF_Ekin: + E.negf.kinetic + + :NEGF_Ebs: + E.negf.band_structure + + Charges Options: + + :qtot: + charge.electrons + + :zvaltot: + charge.protons + + k-point Options + + :kpoint_scf%k_cell: + BZ.k.Matrix + + :kpoint_scf%k_displ: + BZ.k.Displacement + + +Now for example if we want to recieve the information of Total Energy we could communicate like this: :: + + siesta.receive({"E.total"}) + +If we want to send some information to siesta we could communicate like this: :: + + siesta.send({"MD.MaxDispl"}) + + + + + + + + + + + + +Classes +------- + + +MDStep +...... + +The MDStep class retains information on a single MD step. Such a step may be represented by numerous quantities. One may always add new information, but it may for instance be used to retain information such as: + (1) **R** , the atomic coordinates + (2) **V** , the velocities + (3) **F** , the forces + (4) **E** , an energy associated with the current step. + +Array +..... + +Array Class is a generic implementation of ND arrays in pure Lua. This module tries to be as similar to the Python numpy package as possible. Due to everything being in Lua there are not *views* of arrays which means that many functions creates unnecessary data-duplications. This may be leveraged in later code implementat ons. The underlying Array class is implemented as follows: + + (1) Every Array gets associated a `Shape` which determines the size of the current Array. + (2) If the Array is > 1D all elements `Array[i]` is an array with sub-Arrays of one less dimension. + (3) This enables one to call any Array function on sub-partitions of the Array without having to think about the details. + (4) The special case is the last dimension which contains the actual data. The `Array` class is using the same names as the Python numerical library `numpy` for clarity. + + +Shape +..... + +Implementation of Shape to control the size of arrays (@see Array) @classmod Shape A helper class for managing the size of `Array's`. + +Having the Shape of an array in a separate class makes it much easier to implement a flexible interface for interacting with Arrays. A Shape is basically a table which defines the size of the Array +the dimensions of the Array is `#Shape` while each axis size may be queried by `Shape[axis]`. +Additionally a Shape may have a single dimension with size `0` which may only be used to align two shapes, i.e. the `0` axis is inferred from the total size of the aligning Shape. + +Optimizer +......... + +Basic optimization class that is to be inherited by all the optimization classes. + +CG +.. + +An implementation of the conjugate gradient optimization algorithm. This class implements 4 different variations of CG defined by the so-called beta-parameter: + + (1) Polak-Ribiere + (2) Fletcher-Reeves + (3) Hestenes-Stiefel + (4) Dai-Yuan + +Additionally this CG implementation defaults to a beta-damping factor to achieve a smooth restart method, instead of abrupt CG restarts when `beta < 0`, for instance. + +FIRE +.... + +The implementation has several options related to the original method. + +The `FIRE` optimizer implements several variations of the original FIRE algorithm. + +Here we allow to differentiate on how to normalize the displacements: + + (1) `correct` (argument for `FIRE:new`) + (2) "global" perform a global normalization of the coordinates (maintain displacement direction) + (3) "local" perform a local normalization (for each direction of each atom) (displacement direction is not maintained) + (4) `direction` (argument for `FIRE:new`) + (5) "global" perform a global normalization of the velocities (maintain gradient direction) + (6) "local" perform a local normalization of the velocity (for each atom) (gradient direction is not maintained) This `FIRE` optimizer allows two variations of the scaling of the velocities and the resulting displacement. + +LBFGS +..... + +This class contains implementation of the limited memory BFGS algorithm. +The LBFGS algorithm is a straight-forward optimization algorithm which requires very few arguments for a succesful optimization. The most important parameter is the initial Hessian value, which for large values (close to 1) may have difficulties in converging because it is more aggressive (keeps more of the initial gradient). The default value is rather safe and should enable optimization on most systems. This optimization method also implements a history-discard strategy, if needed, for possible speeding up the convergence. A field in the argument table, `discard`, may be passed which takes one of: + +(1) "none", no discard strategy +(2) "max-dF", if a displacement is being made beyond the max-displacement we do not store the step in the history + +This optimization method also implements a scaling strategy, if needed, for possible speeding up the convergence. A field in the argument table, `scaling`, may be passed which takes one of: + +(1) "none", no scaling strategy used +(2) "initial", only the initial inverse Hessian and use that in all subsequent iterations +(3) "every", scale for every step + +LINE +.... + +This class conatins implementation of a line minimizer algorithm. The `Line` class optimizes a set of parameters for a function such that the gradient projected onto a gradient-direction will be minimized. I.e. it finds the minimum of a function on a gradient line such that the true gradient is orthogonal to the direction. A simple implementation of a line minimizer. This line-minimization algorithm may use any (default to `LBFGS`) optimizer and will optimize a given direction by projecting the gradient onto an initial gradient direction. + +NEB +... + +NEB class Instantiating a new `NEB` object. For the `NEB` object it is important to pass the images, and _then_ all the NEB settings as named arguments in a table. + +-- The `NEB` object implements a generic NEB algorithm as detailed in: + +(1) "Improved tangent estimate in the nudged elastic band method for finding minimum energy paths and saddle points", Henkelman & Jonsson, JCP (113), 2000 +(2) "A climbing image nudged elastic band method for finding saddle points and minimum energy paths", Henkelman, Uberuaga, & Jonsson, JCP (113), 2000 + +.. NOTE:: + This particular implementation has been tested and initially developed by Jesper T. Rasmussen, DTU Nanotech, 2016. + +When instantiating a new `NEB` calculator one _must_ populate the initial, all intermediate images and a final image in a a table. The easiest way to do this can be seen in the below usage field. To perform the NEB calculation all images (besides the initial and final) are relaxed by an external relaxation method (see `Optimizer` and its child classes). Due to the forces being highly non-linear as the NEB algorithm updates the forces depending on the nearest images, it is adviced to use an MD-like relaxation method such as `FIRE`. If one uses history based relaxation methods (`LBFGS`, `CG`, etc.) one should limit the number of history steps used. Running the NEB class will create a huge list of files with corresponding output. Check the `NEB:save` function for details. + + +DNEB +.... + +A modification of the nudged elastic band NEB method is implementation enables stable optimizations to be run using both the limited-memory Broyden–Fletcher–Goldfarb–Shanno~L-BFGS. quasi-Newton and slow-response quenched velocity Verlet minimizers. The DNEB bject implements a generic DNEB algorithm as detailed in: + +- "A doubly nudged elastic band method for finding transition states", Semen A. Trygubenkoa and David J. Wales , J. Chem. Phys., Vol. 120, No. 5, 1 February 2004. + + +VCNEB +..... +The VC-NEB method is a more general tool for exploring the activation paths between the two end points of a phase transition process within a larger configuration space. The VC-NEB object implements a generic VC-NEB algorithm as detailed in: + +- "Variable cell nudged elastic band method for studying solid–solid structural phase transitions" ,G.-R.Qianetal, Computer Physics Communications 184 (2013) 2111–2118. + +TNEB +.... + +TNEB is a method to introduce temperature corrections to a minimum-energyreaction path. The method is based on the maximization of the flux for the Smoluchowski equationand it is implemented using a nudged-elastic-band algorithm. + +The TNEB object implements a generic TNEB algorithm as detailed in: + +- "A temperature-dependent nudged-elastic-band algorithm", Ramon Crehuet and Martin J. Field,The Journal of Chemical Physics 118, 9563 (2003); doi: 10.1063/1.1571817 + + diff --git a/Docs/source/content/images/1.png b/Docs/source/content/images/1.png new file mode 100755 index 0000000..b4fbe12 Binary files /dev/null and b/Docs/source/content/images/1.png differ diff --git a/Docs/source/content/images/2.png b/Docs/source/content/images/2.png new file mode 100755 index 0000000..f4d9b30 Binary files /dev/null and b/Docs/source/content/images/2.png differ diff --git a/Docs/source/content/images/3.png b/Docs/source/content/images/3.png new file mode 100755 index 0000000..c00c89c Binary files /dev/null and b/Docs/source/content/images/3.png differ diff --git a/Docs/source/content/setting-up-flos.rst b/Docs/source/content/setting-up-flos.rst new file mode 100644 index 0000000..8443398 --- /dev/null +++ b/Docs/source/content/setting-up-flos.rst @@ -0,0 +1,113 @@ +Setting Up FLOS for SIESTA +========================== +Installation of FLOS +-------------------- + +.. figure:: ./images/1.png + :width: 400px + + Flook Architecture + +Requirements +............ + +The only requirement is the Lua language. +The require Lua version is 5.3. However, if you are stuck with Lua 5.2 you can apply this patch :: + + patch -p1 < lua_52.patch + +.. NOTE:: + + For sure running siesta with lua needs the compilation of siesta with flook library, which enabling the fortran lua hook (flook) that we will discusse () section. + + +Downloading and Installation of FLOS +.................................... + +This Lua library may be used out of the box. To enable the use of this library you only require the LUA_PATH to contain the path to the library. +Importantly this library requires an explicit /?/init.lua definition. As an example the following bash commands enables the library :: + + cd $HOME + git clone https://github.com/siesta-project/flos.git + cd flos + git submodule init + git submodule update + export LUA_PATH="$HOME/flos/?.lua;$HOME/flos/?/init.lua;$LUA_PATH;;" + +and that is it. Now you can use the flos library. + + +Enabling SIESTA LUA interface (FLOOK) +------------------------------------- +As we mentioned we have to compile siesta with flook library. + +Downloading and installation FLOOK +.................................. +Installing flook requires you to first fetch the library which is currently hosted at github at flook. +To fetch all required files do this: :: + + git clone https://github.com/ElectronicStructureLibrary/flook.git + cd flook + git submodule init + git submodule update + +Now depending of compiler Vendor you have two options: :: + +* gfortran +* ifort + +To compile with gfortran do this: :: + + make VENDOR=gfortran + make liball VENDOR=gfortran + +To compile with ifort do this: :: + + make VENDOR=intel + make liball VENDOR=intel + +After compiling you we have above libs which needed for compiling siesta: :: + + flook.mod + libflook.a + libflookall.a + +Downloading and Compiling SIESTA with FLOOK +........................................... + +To Get the latest version of SIESTA from gitlab: :: + + git clone git@gitlab.com:siesta-project/siesta.git + +Go to siesta folder: :: + + cd siesta + +Now make folder Obj-* and go to the folder: :: + + ~/siesta$ mkdir Obj-lua + ~/siesta$ cd Obj-lua + +.. NOTE:: + + Here Obj-* = Obj-lua + +Now setup up your Obj-lua folder like this: :: + + ~/siesta/Obj-lua$ sh ../Src/obj_setup.sh + +In this step we have to make our arch.make file, here we use the (``gfortran.make``) file in (``Obj``) Folder. We need to append the following lines to our arch.make: :: + + INCFLAGS += -I/{PUT YOUR FLOOK ROOT PATH} + LDFLAGS +=-L/{PUT YOUR FLOOK ROOT PATH} -Wl,-rpath={PUT YOUR FLOOK ROOT PATH} + LIBS+= -lflookall -ldl + COMP_LIBS += libfdict.a + FPPFLAGS += -DSIESTA__FLOOK + +Now everthing ready to compile siesta : :: + + ~/siesta/Obj-lua$ make + +After Compilation you should have siesta binary. + + diff --git a/Docs/source/content/tutorials.rst b/Docs/source/content/tutorials.rst new file mode 100644 index 0000000..a6da680 --- /dev/null +++ b/Docs/source/content/tutorials.rst @@ -0,0 +1,1716 @@ +Tutorials of FLOS +================= + +.. figure:: ./images/3.png + :width: 400px + + What Flos Could Do...! + +Basics +------ + +To Run Siesta with LUA functionality, has threefold steps: + (1) providing lua script in the same run folder (alongside fdf and pseudos) for a particular task. + (2) Set the MD.TypeOfRun to LUA + (3) add the lua script in fdf file using this flag : Lua.Script + +.. NOTE:: + + Following Examples are only the content and structure of lua script files. All the examples could be found in the tutorial folder. + +Optimizations +------------- + +Mech Cutoff +........... + +This tutorial can take any system and will perform a series of calculations with increasing +Mesh.Cutoff and it will write-out a table file to be plotted which contains the Mesh.Cutoff vs Energy. + +The task steps is the following: + (1) Read Starting Mesh cutoff (``siesta.state= siesta.INITIALIZE`` ) + (2) Run siesta with the Starting Mesh (``siesta.state= siesta.INI_MD`` ) + (3) Save the Mesh and Enegy then increase the Mesh cutoff and Run siesta with new mesh (``siesta.state == siesta.MOVE``) and (user defined function) + (4) If reach to last mesh write Mesh cutoff vs Energy in file (``siesta.state == siesta.ANALYSIS``) + +For optimizing our mesh we may need 3 values: + + (1) cutoff_start + (2) cutoff_end + (3) cutoff_step + +To do so we have these lines in our script: :: + + -- Load the FLOS module + local flos = require "flos" + + local cutoff_start = 150. + local cutoff_end = 650. + local cutoff_step = 50. + + -- Create array of cut-offs + local cutoff = flos.Array.range(cutoff_start, cutoff_end, cutoff_step) + local Etot = flos.Array.zeros(#cutoff) + -- Initial cut-off element + local icutoff = 1 + +.. NOTE:: + + In above lines we use flos array class to generate our array cutoffs + +For user defined function we have: :: + + function step_cutoff(cur_cutoff) + if icutoff < cutoff then + icutoff = icutoff + 1 + else + return false + end + if cutoff[icutoff] <= cur_cutoff then + cutoff[icutoff] = cutoff[icutoff-1] + Etot[icutoff] = Etot[icutoff-1] + return step_cutoff(cur_cutoff) + end + return true + end + +Which only increase the value of mesh with step value cur_cutoff. + +Now we are ready to write our main siesta communicator function: :: + + function siesta_comm() + -- Do the actual communication with SIESTA + if siesta.state == siesta.INITIALIZE then + -- In the initialization step we request the + -- Mesh cutoff (merely to be able to set it + siesta.receive({"Mesh.Cutoff.Minimum"}) + -- Overwrite to ensure we start from the beginning + siesta.Mesh.Cutoff.Minimum = cutoff[icutoff] + IOprint( ("\nLUA: starting mesh-cutoff: %8.3f Ry\n"):format(cutoff[icutoff]) ) + siesta.send({"Mesh.Cutoff.Minimum"}) + end + if siesta.state == siesta.INIT_MD then + siesta.receive({"Mesh.Cutoff.Used"}) + -- Store the used meshcutoff for this iteration + cutoff[icutoff] = siesta.Mesh.Cutoff.Used + end + if siesta.state == siesta.MOVE then + -- Retrieve the total energy and update the + -- meshcutoff for the next cycle + -- Notice, we do not move, or change the geometry + -- or cell-vectors. + siesta.receive({"E.total","MD.Relaxed"}) + Etot[icutoff] = siesta.E.total + -- Step the meshcutoff for the next iteration + if step_cutoff(cutoff[icutoff]) then + siesta.Mesh.Cutoff.Minimum = cutoff[icutoff] + else + siesta.MD.Relaxed = true + end + siesta.send({"Mesh.Cutoff.Minimum","MD.Relaxed"}) + end + if siesta.state == siesta.ANALYSIS then + local file = io.open("meshcutoff_E.dat", "w") + file:write("# Mesh-cutoff vs. energy\n") + -- We write out a table with mesh-cutoff, the difference between + -- the last iteration, and the actual value + file:write( ("%8.3e %17.10e %17.10e\n"):format(cutoff[1], 0., Etot[1]) ) + for i = 2, #cutoff do + file:write( ("%8.3e %17.10e %17.10e\n"):format(cutoff[i], Etot[i]-Etot[i-1], Etot[i]) ) + end + file:close() + end + + +.. NOTE:: + The important thing to take away is that, siesta in ``siesta.MOVE`` remains to that state unless we ``siesta.MD.Relaxed = true`` . + +k points +........ + +This example will perform a series of calculations with increasing +k-Mesh and it will write-out a table file to be plotted which contains the k-Mesh vs Energy. + +The Initialization is : :: + + local kpoint_start_x = 1. + local kpoint_end_x = 10. + local kpoint_step_x = 3. + local kpoint_start_y = 1. + local kpoint_end_y = 10 + local kpoint_step_y = 3. + local kpoint_start_z = 1. + local kpoint_end_z = 1. + local kpoint_step_z = 1. + local flos = require "flos" + local kpoint_cutoff_x = flos.Array.range(kpoint_start_x, kpoint_end_x, kpoint_step_x) + local kpoint_cutoff_y = flos.Array.range(kpoint_start_y, kpoint_end_y, kpoint_step_y) + local kpoint_cutoff_z = flos.Array.range(kpoint_start_z, kpoint_end_z, kpoint_step_z) + local Total_kpoints = flos.Array.zeros(3) + Total_kpoints[1] = math.max(#kpoint_cutoff_x) + Total_kpoints[2] = math.max(#kpoint_cutoff_y) + Total_kpoints[3] = math.max(#kpoint_cutoff_z) + local kpoints_num = Total_kpoints:max() + local kpoint_mesh = flos.Array.zeros(9) + kpoint_mesh = kpoint_mesh:reshape(3,3) + local Etot = flos.Array.zeros(kpoints_num) + local ikpoint_x = 1 + local ikpoint_y = 1 + local ikpoint_z = 1 + local kpoints_num_temp = 0 + +For user defined function we have: :: + + function step_kpointf_x(cur_kpoint_x) + if ikpoint_x < #kpoint_cutoff_x then + ikpoint_x = ikpoint_x + 1 + else + return false + end + if kpoint_cutoff_x[ikpoint_x] <= cur_kpoint_x then + kpoint_cutoff_x[ikpoint_x] = kpoint_cutoff_x[ikpoint_x-1] + Etot[ikpoint_x] = Etot[ikpoint_x-1] + return step_kpointf_x(cur_kpoint_x) + end + + return true + end + + function step_kpointf_y(cur_kpoint_y) + if ikpoint_y < #kpoint_cutoff_y then + ikpoint_y = ikpoint_y + 1 + else + return false + end + if kpoint_cutoff_y[ikpoint_y] <= cur_kpoint_y then + kpoint_cutoff_y[ikpoint_y] = kpoint_cutoff_y[ikpoint_y-1] + Etot[ikpoint_y] = Etot[ikpoint_y-1] + return step_kpointf_y(cur_kpoint_y) + end + return true + end + + function step_kpointf_z(cur_kpoint_z) + if ikpoint_z < #kpoint_cutoff_z then + ikpoint_z = ikpoint_z + 1 + else + return false + end + if kpoint_cutoff_z[ikpoint_z] <= cur_kpoint_z then + kpoint_cutoff_z[ikpoint_z] = kpoint_cutoff_x[ikpoint_z-1] + Etot[ikpoint_z] = Etot[ikpoint_z-1] + return step_kpointf_z(cur_kpoint_z) + end + return true + end + +For our main siesta communicator function we have: :: + + function siesta_comm() + + if siesta.state == siesta.INITIALIZE then + siesta.receive({"BZ.k.Matrix"}) + kpoints = flos.Array.from(siesta.BZ.k.Matrix) + IOprint ("LUA: Provided k-point :" )--.. tostring( kpoints_num)) + kpoint_mesh = kpoints + IOprint("LUA: k_x :\n" .. tostring(kpoint_cutoff_x)) + IOprint("LUA: k_y :\n" .. tostring(kpoint_cutoff_y)) + IOprint("LUA: k_z :\n" .. tostring(kpoint_cutoff_z)) + IOprint("LUA: Total Number of k-points :" .. tostring(Total_kpoints:max() )) + kpoint_mesh[1][1] = kpoint_start_x + kpoint_mesh[2][2] = kpoint_start_y + kpoint_mesh[3][3] = kpoint_start_y + IOprint ("LUA: Number of k-points (".. tostring(kpoints_num_temp+1) .. "/" .. tostring(Total_kpoints:max()).. ")" ) + IOprint("LUA: Starting Kpoint :\n" .. tostring(kpoint_mesh)) + siesta.BZ.k.Matrix = kpoint_mesh + siesta.send({"BZ.k.Matrix"}) + end + + if siesta.state == siesta.INIT_MD then + + siesta.receive({"BZ.k.Matrix"}) + end + + if siesta.state == siesta.MOVE then + + siesta.receive({"E.total", + "MD.Relaxed"}) + + Etot[ikpoint_x ] = siesta.E.total + + if step_kpointf_x(kpoint_cutoff_x[ikpoint_x]) then + kpoint_mesh[1][1] = kpoint_cutoff_x[ikpoint_x] + if step_kpointf_y(kpoint_cutoff_y[ikpoint_y]) then + kpoint_mesh[2][2] = kpoint_cutoff_y[ikpoint_y] + if step_kpointf_z(kpoint_cutoff_z[ikpoint_z]) then + kpoint_mesh[3][3] = kpoint_cutoff_z[ikpoint_z] + end + end + end + + siesta.BZ.k.Matrix = kpoint_mesh + + kpoints_num_temp = kpoints_num_temp + 1 + if kpoints_num == kpoints_num_temp then + siesta.MD.Relaxed = true + else + + IOprint ("LUA: Number of k-points (".. tostring(kpoints_num_temp+1) .. "/" .. tostring(Total_kpoints:max()).. ")" ) + IOprint("LUA: Next Kpoint to Be Used :\n" .. tostring(siesta.BZ.k.Matrix)) + end + + siesta.send({"BZ.k.Matrix", "MD.Relaxed"}) + + end + + if siesta.state == siesta.ANALYSIS then + local file = io.open("k_meshcutoff_E.dat", "w") + file:write("# kpoint-Mesh-cutoff vs. energy\n") + file:write( ("%8.3e %17.10e %17.10e\n"):format(1, Etot[1], 0.) ) + for i = 2, Total_kpoints:max() do + file:write( ("%8.3e %17.10e %17.10e\n"):format(i,Etot[i], Etot[i]-Etot[i-1]) ) + end + file:close() + end + + +Relaxations +----------- + +Whithin Lua we could have plenty of options for Relaxations. Below there are couple of those methods to apply. + + +Cell Relaxation +................... +This example can take any geometry and will relax the +cell vectors according to the siesta input options: + + - MD.MaxStressTol + - MD.MaxDispl + +This example defaults to two simultaneous LBFGS algorithms +which seems adequate in most situations. + +For user defined function we have move function which take care of relaxations part: :: + + function siesta_move(siesta) + + local cell = flos.Array.from(siesta.geom.cell) / Unit.Ang + local xa = flos.Array.from(siesta.geom.xa) / Unit.Ang + local tmp = -flos.Array.from(siesta.geom.stress) * Unit.Ang ^ 3 / Unit.eV + local stress = flos.Array.empty(6) + stress[1] = tmp[1][1] + stress[2] = tmp[2][2] + stress[3] = tmp[3][3] + stress[4] = (tmp[2][3] + tmp[3][2]) * 0.5 + stress[5] = (tmp[1][3] + tmp[3][1]) * 0.5 + stress[6] = (tmp[1][2] + tmp[2][1]) * 0.5 + tmp = nil + stress = stress * stress_mask + local vol = cell[1]:cross(cell[2]):dot(cell[3]) + local all_strain = {} + local weight = flos.Array.empty(#LBFGS) + for i = 1, #LBFGS do + all_strain[i] = LBFGS[i]:optimize(strain, stress * vol) + LBFGS[i]:optimized(stress) + weight[i] = LBFGS[i].weight + end + + weight = weight / weight:sum() + if #LBFGS > 1 then + IOprint("\nLBFGS weighted average: ", weight) + end + + local out_strain = all_strain[1] * weight[1] + local relaxed = LBFGS[1]:optimized() + for i = 2, #LBFGS do + out_strain = out_strain + all_strain[i] * weight[i] + relaxed = relaxed and LBFGS[i]:optimized() + end + all_strain = nil + + strain = out_strain * stress_mask + out_strain = nil + + local dcell = flos.Array( cell.shape ) + dcell[1][1] = 1.0 + strain[1] + dcell[1][2] = 0.5 * strain[6] + dcell[1][3] = 0.5 * strain[5] + dcell[2][1] = 0.5 * strain[6] + dcell[2][2] = 1.0 + strain[2] + dcell[2][3] = 0.5 * strain[4] + dcell[3][1] = 0.5 * strain[5] + dcell[3][2] = 0.5 * strain[4] + dcell[3][3] = 1.0 + strain[3] + + local out_cell = cell_first:dot(dcell) + dcell = nil + + weight = weight / weight:sum() + if #LBFGS > 1 then + IOprint("\nLBFGS weighted average: ", weight) + end + + local out_strain = all_strain[1] * weight[1] + local relaxed = LBFGS[1]:optimized() + for i = 2, #LBFGS do + out_strain = out_strain + all_strain[i] * weight[i] + relaxed = relaxed and LBFGS[i]:optimized() + end + all_strain = nil + + strain = out_strain * stress_mask + out_strain = nil + + local dcell = flos.Array( cell.shape ) + dcell[1][1] = 1.0 + strain[1] + dcell[1][2] = 0.5 * strain[6] + dcell[1][3] = 0.5 * strain[5] + dcell[2][1] = 0.5 * strain[6] + dcell[2][2] = 1.0 + strain[2] + dcell[2][3] = 0.5 * strain[4] + dcell[3][1] = 0.5 * strain[5] + dcell[3][2] = 0.5 * strain[4] + dcell[3][3] = 1.0 + strain[3] + + local out_cell = cell_first:dot(dcell) + dcell = nil + + local lat = flos.Lattice:new(cell) + local fxa = lat:fractional(xa) + xa = fxa:dot(out_cell) + lat = nil + fxa = nil + + siesta.geom.cell = out_cell * Unit.Ang + siesta.geom.xa = xa * Unit.Ang + siesta.MD.Relaxed = relaxed + + return {"geom.cell", + "geom.xa", + "MD.Relaxed"} + end + +For our main siesta communicator function we have: :: + + function siesta_comm() + + local ret_tbl = {} + + if siesta.state == siesta.INITIALIZE then + + siesta.receive({"geom.cell", + "MD.Relax.Cell", + "MD.MaxDispl", + "MD.MaxStressTol"}) + + if not siesta.MD.Relax.Cell then + + siesta.MD.Relax.Cell = true + ret_tbl = {"MD.Relax.Cell"} + + end + + IOprint("\nLUA convergence information for the LBFGS algorithms:") + + cell_first = flos.Array.from(siesta.geom.cell) / Unit.Ang + + for i = 1, #LBFGS do + LBFGS[i].tolerance = siesta.MD.MaxStressTol * Unit.Ang ^ 3 / Unit.eV + LBFGS[i].max_dF = siesta.MD.MaxDispl / Unit.Ang + + if siesta.IONode then + LBFGS[i]:info() + end + end + + end + + if siesta.state == siesta.MOVE then + siesta.receive({"geom.cell", + "geom.xa", + "geom.stress", + "MD.Relaxed"}) + ret_tbl = siesta_move(siesta) + end + + siesta.send(ret_tbl) + end + + +Cell and Geometry Relaxation +............................ + +This example can take any geometry and will relax the +cell vectors according to the siesta input options: + + - MD.MaxForceTol + - MD.MaxStressTol + - MD.MaxCGDispl + +To initiate we have : :: + + local flos = require "flos" + + -- Create the two LBFGS algorithms with + -- initial Hessians 1/75 and 1/50 + local geom = {} + geom[1] = flos.LBFGS{H0 = 1. / 75.} + geom[2] = flos.LBFGS{H0 = 1. / 50.} + + local lattice = {} + lattice[1] = flos.LBFGS{H0 = 1. / 75.} + lattice[2] = flos.LBFGS{H0 = 1. / 50.} + + -- Grab the unit table of siesta (it is already created + -- by SIESTA) + local Unit = siesta.Units + + -- Initial strain that we want to optimize to minimize + -- the stress. + local strain = flos.Array.zeros(6) + -- Mask which directions we should relax + -- [xx, yy, zz, yz, xz, xy] + -- Default to all. + local stress_mask = flos.Array.ones(6) + + -- To only relax the diagonal elements you may do this: + stress_mask[4] = 0. + stress_mask[5] = 0. + stress_mask[6] = 0. + + -- The initial cell + local cell_first + + -- This variable controls which relaxation is performed + -- first. + -- If true, it starts by relaxing the geometry (coordinates) + -- (recommended) + -- If false, it starts by relaxing the cell vectors. + local relax_geom = true + +For user defined function we have move couple of functions. The Fucntion which take care of Stress part is : :: + + function stress_from_voigt(voigt) + + local stress = flos.Array.empty(3, 3) + stress[1][1] = voigt[1] + stress[1][2] = voigt[6] + stress[1][3] = voigt[5] + stress[2][1] = voigt[6] + stress[2][2] = voigt[2] + stress[2][3] = voigt[4] + stress[3][1] = voigt[5] + stress[3][2] = voigt[4] + stress[3][3] = voigt[3] + + return stress + end + +The Function which take care of geometry relaxations part: :: + + function siesta_geometry(siesta) + + local xa = siesta.geom.xa + local fa = siesta.geom.fa + + local all_xa = {} + local weight = flos.Array.empty(#geom) + for i = 1, #geom do + all_xa[i] = geom[i]:optimize(xa, fa) + weight[i] = geom[i].weight + end + + weight = weight / weight:sum() + if #geom > 1 then + IOprint("\nGeometry weighted average: ", weight) + end + + local out_xa = all_xa[1] * weight[1] + for i = 2, #geom do + out_xa = out_xa + all_xa[i] * weight[i] + end + all_xa = nil + + siesta.geom.xa = out_xa * Unit.Ang + + return {"geom.xa"} + end + +The Function which take care of cell relaxations part: :: + + function siesta_cell(siesta) + + local cell = siesta.geom.cell + local xa = siesta.geom.xa + local stress = stress_to_voigt(siesta.geom.stress) + stress = stress * stress_mask + + local vol = cell[1]:cross(cell[2]):dot(cell[3]) + + local all_strain = {} + local weight = flos.Array.empty(#lattice) + for i = 1, #lattice do + all_strain[i] = lattice[i]:optimize(strain, stress * vol) + lattice[i]:optimized(stress) + weight[i] = lattice[i].weight + end + + weight = weight / weight:sum() + if #lattice > 1 then + IOprint("\nLattice weighted average: ", weight) + end + + local out_strain = all_strain[1] * weight[1] + for i = 2, #lattice do + out_strain = out_strain + all_strain[i] * weight[i] + end + all_strain = nil + + strain = out_strain * stress_mask + out_strain = nil + + local dcell = flos.Array( cell.shape ) + dcell[1][1] = 1.0 + strain[1] + dcell[1][2] = 0.5 * strain[6] + dcell[1][3] = 0.5 * strain[5] + dcell[2][1] = 0.5 * strain[6] + dcell[2][2] = 1.0 + strain[2] + dcell[2][3] = 0.5 * strain[4] + dcell[3][1] = 0.5 * strain[5] + dcell[3][2] = 0.5 * strain[4] + dcell[3][3] = 1.0 + strain[3] + + local out_cell = cell_first:dot(dcell) + dcell = nil + + local lat = flos.Lattice:new(cell) + local fxa = lat:fractional(xa) + xa = fxa:dot(out_cell) + lat = nil + fxa = nil + + siesta.geom.cell = out_cell * Unit.Ang + siesta.geom.xa = xa * Unit.Ang + + return {"geom.cell", + "geom.xa"} + end + + +For our main siesta communicator function we have: :: + + function siesta_comm() + + local ret_tbl = {} + + if siesta.state == siesta.INITIALIZE then + siesta.receive({"geom.cell", + "MD.Relax.Cell", + "MD.MaxDispl", + "MD.MaxForceTol", + "MD.MaxStressTol"}) + + if not siesta.MD.Relax.Cell then + + siesta.MD.Relax.Cell = true + ret_tbl = {"MD.Relax.Cell"} + + end + + IOprint("\nLUA convergence information for the LBFGS algorithms:") + + cell_first = flos.Array.from(siesta.geom.cell) / Unit.Ang + + IOprint("Lattice optimization:") + for i = 1, #lattice do + lattice[i].tolerance = siesta.MD.MaxStressTol * Unit.Ang ^ 3 / Unit.eV + lattice[i].max_dF = siesta.MD.MaxDispl / Unit.Ang + + if siesta.IONode then + lattice[i]:info() + end + end + + IOprint("\nGeometry optimization:") + for i = 1, #geom do + geom[i].tolerance = siesta.MD.MaxForceTol * Unit.Ang / Unit.eV + geom[i].max_dF = siesta.MD.MaxDispl / Unit.Ang + + if siesta.IONode then + geom[i]:info() + end + end + + if relax_geom then + IOprint("\nLUA: Starting with geometry relaxation!\n") + else + IOprint("\nLUA: Starting with cell relaxation!\n") + end + + end + + if siesta.state == siesta.MOVE then + + siesta.receive({"geom.cell", + "geom.xa", + "geom.fa", + "geom.stress", + "MD.Relaxed"}) + ret_tbl = siesta_move(siesta) + end + + siesta.send(ret_tbl) + end + +For the Move Part we have : :: + + function siesta_move(siesta) + siesta.geom.cell = flos.Array.from(siesta.geom.cell) / Unit.Ang + siesta.geom.xa = flos.Array.from(siesta.geom.xa) / Unit.Ang + siesta.geom.fa = flos.Array.from(siesta.geom.fa) * Unit.Ang / Unit.eV + siesta.geom.stress = -flos.Array.from(siesta.geom.stress) * Unit.Ang ^ 3 / Unit.eV + + local voigt = stress_to_voigt(siesta.geom.stress) + voigt = voigt * stress_mask + local conv_lattice = lattice[1]:optimized(voigt) + voigt = nil + + local conv_geom = geom[1]:optimized(siesta.geom.fa) + + if conv_lattice and conv_geom then + + siesta.MD.Relaxed = true + return {'MD.Relaxed'} + + end + + if relax_geom and conv_geom then + + relax_geom = false + for i = 1, #geom do + geom[i]:reset() + end + + cell_first = siesta.geom.cell:copy() + + IOprint("\nLUA: switching to cell relaxation!\n") + + elseif (not relax_geom) and conv_lattice then + + relax_geom = true + for i = 1, #lattice do + lattice[i]:reset() + end + + IOprint("\nLUA: switching to geometry relaxation!\n") + + end + + if relax_geom then + return siesta_geometry(siesta) + else + return siesta_cell(siesta) + end + + end + + + +Geometry Relaxation with CG +........................... + +This example can take any geometry and will relax it +according to the siesta input options: + + - MD.MaxForceTol + - MD.MaxCGDispl + +One should note that the CG algorithm first converges +when the total force (norm) on the atoms are below the +tolerance. This is contrary to the SIESTA default which +is a force tolerance for the individual directions, +i.e. max-direction force. + +This example is prepared to easily create +a combined relaxation of several CG algorithms +simultaneously. In some cases this is shown to +speed up the convergence because an average is taken +over several optimizations. + +The Initialization is : :: + + local flos = require "flos" + + local CG = {} + CG[1] = flos.CG{beta='PR', line=flos.Line{optimizer = flos.LBFGS{H0 = 1. / 75.} } } + CG[2] = flos.CG{beta='PR', line=flos.Line{optimizer = flos.LBFGS{H0 = 1. / 50.} } } + local Unit = siesta.Units + +For the Move Part we have : :: + + function siesta_move(siesta) + + local xa = flos.Array.from(siesta.geom.xa) / Unit.Ang + local fa = flos.Array.from(siesta.geom.fa) * Unit.Ang / Unit.eV + + local all_xa = {} + local weight = flos.Array.empty(#CG) + for i = 1, #CG do + all_xa[i] = CG[i]:optimize(xa, fa) + weight[i] = CG[i].weight + + end + + weight = weight / weight:sum() + if #CG > 1 then + IOprint("\nCG weighted average: ", weight) + end + + local out_xa = all_xa[1] * weight[1] + local relaxed = CG[1]:optimized() + for i = 2, #CG do + + out_xa = out_xa + all_xa[i] * weight[i] + relaxed = relaxed and CG[i]:optimized() + + end + all_xa = nil + + siesta.geom.xa = out_xa * Unit.Ang + siesta.MD.Relaxed = relaxed + + return {"geom.xa", + "MD.Relaxed"} + end + +For our main siesta communicator function we have: :: + + function siesta_comm() + + local ret_tbl = {} + + if siesta.state == siesta.INITIALIZE then + siesta.receive({"MD.MaxDispl", + "MD.MaxForceTol"}) + + IOprint("\nLUA convergence information for the LBFGS algorithms:") + for i = 1, #CG do + CG[i].tolerance = siesta.MD.MaxForceTol * Unit.Ang / Unit.eV + CG[i].max_dF = siesta.MD.MaxDispl / Unit.Ang + CG[i].line.tolerance = CG[i].tolerance + CG[i].line.max_dF = CG[i].max_dF -- this is not used + CG[i].line.optimizer.tolerance = CG[i].tolerance -- this is not used + CG[i].line.optimizer.max_dF = CG[i].max_dF -- this is used + if siesta.IONode then + CG[i]:info() + end + end + + end + + if siesta.state == siesta.MOVE then + siesta.receive({"geom.xa", + "geom.fa", + "MD.Relaxed"}) + ret_tbl = siesta_move(siesta) + end + + siesta.send(ret_tbl) + end + + +Geometry Relaxation with Fire +............................. + +This example can take any geometry and will relax it +according to the siesta input options: + + - MD.MaxForceTol + - MD.MaxCGDispl + +One should note that the FIRE algorithm first converges +when the total force (norm) on the atoms are below the +tolerance. This is contrary to the SIESTA default which +is a force tolerance for the individual directions, +i.e. max-direction force. + +The Initialization is : :: + + local flos = require "flos" + local FIRE = {} + local dt_init = 0.5 + FIRE[1] = flos.FIRE{dt_init = dt_init, direction="global", correct="local"} + FIRE[2] = flos.FIRE{dt_init = dt_init, direction="global", correct="global"} + FIRE[3] = flos.FIRE{dt_init = dt_init, direction="local", correct="local"} + FIRE[4] = flos.FIRE{dt_init = dt_init, direction="local", correct="global"} + local Unit = siesta.Units + +For the Move Part we have : :: + + function siesta_move(siesta) + + local xa = flos.Array.from(siesta.geom.xa) / Unit.Ang + local fa = flos.Array.from(siesta.geom.fa) * Unit.Ang / Unit.eV + + local all_xa = {} + local weight = flos.Array.empty(#FIRE) + for i = 1, #FIRE do + all_xa[i] = FIRE[i]:optimize(xa, fa) + weight[i] = FIRE[i].weight + + end + + weight = weight / weight:sum() + if #FIRE > 1 then + IOprint("\nFIRE weighted average: ", weight) + end + + local out_xa = all_xa[1] * weight[1] + local relaxed = FIRE[1]:optimized() + for i = 2, #FIRE do + out_xa = out_xa + all_xa[i] * weight[i] + relaxed = relaxed and FIRE[i]:optimized() + end + all_xa = nil + + siesta.geom.xa = out_xa * Unit.Ang + siesta.MD.Relaxed = relaxed + + return {"geom.xa", + "MD.Relaxed"} + end + +For our main siesta communicator function we have: :: + + function siesta_comm() + + local ret_tbl = {} + + if siesta.state == siesta.INITIALIZE then + + siesta.receive({"MD.MaxDispl", + "MD.MaxForceTol", + "geom.mass"}) + + IOprint("\nLUA convergence information for the FIRE algorithms:") + for i = 1, #FIRE do + + FIRE[i].tolerance = siesta.MD.MaxForceTol * Unit.Ang / Unit.eV + FIRE[i].max_dF = siesta.MD.MaxDispl / Unit.Ang + FIRE[i].set_mass(siesta.geom.mass) + + if siesta.IONode then + FIRE[i]:info() + end + end + end + + if siesta.state == siesta.MOVE then + + siesta.receive({"geom.xa", + "geom.fa", + "MD.Relaxed"}) + + ret_tbl = siesta_move(siesta) + + end + + siesta.send(ret_tbl) + + end + + + +Geometry Relaxation with LBFGS +.............................. + +This example can take any geometry and will relax it +according to the siesta input options: + + - MD.MaxForceTol + - MD.MaxCGDispl + +One should note that the LBFGS algorithm first converges +when the total force (norm) on the atoms are below the +tolerance. This is contrary to the SIESTA default which +is a force tolerance for the individual directions, +i.e. max-direction force. + +The Initialization is : :: + + local flos = require "flos" + + local LBFGS = {} + LBFGS[1] = flos.LBFGS{H0 = 1. / 75.} + LBFGS[2] = flos.LBFGS{H0 = 1. / 50.} + local Unit = siesta.Units + +For the Move Part we have : :: + + function siesta_move(siesta) + + local xa = flos.Array.from(siesta.geom.xa) / Unit.Ang + local fa = flos.Array.from(siesta.geom.fa) * Unit.Ang / Unit.eV + + local all_xa = {} + local weight = flos.Array.empty(#LBFGS) + for i = 1, #LBFGS do + all_xa[i] = LBFGS[i]:optimize(xa, fa) + weight[i] = LBFGS[i].weight + + end + + weight = weight / weight:sum() + if #LBFGS > 1 then + IOprint("\nLBFGS weighted average: ", weight) + end + + local out_xa = all_xa[1] * weight[1] + local relaxed = LBFGS[1]:optimized() + for i = 2, #LBFGS do + out_xa = out_xa + all_xa[i] * weight[i] + relaxed = relaxed and LBFGS[i]:optimized() + + end + all_xa = nil + + siesta.geom.xa = out_xa * Unit.Ang + siesta.MD.Relaxed = relaxed + + return {"geom.xa", + "MD.Relaxed"} + end + +For our main siesta communicator function we have: :: + + function siesta_comm() + + local ret_tbl = {} + if siesta.state == siesta.INITIALIZE then + siesta.receive({"MD.MaxDispl", + "MD.MaxForceTol"}) + + IOprint("\nLUA convergence information for the LBFGS algorithms:") + for i = 1, #LBFGS do + LBFGS[i].tolerance = siesta.MD.MaxForceTol * Unit.Ang / Unit.eV + LBFGS[i].max_dF = siesta.MD.MaxDispl / Unit.Ang + if siesta.IONode then + LBFGS[i]:info() + end + end + + end + + if siesta.state == siesta.MOVE then + siesta.receive({"geom.xa", + "geom.fa", + "MD.Relaxed"}) + ret_tbl = siesta_move(siesta) + + end + + siesta.send(ret_tbl) + end + +Constrained Cell Relaxation +........................... + + +Finding Transition States Minimum Energy Path (MEP) +--------------------------------------------------- + +Nudged Elastic Band +................... +Example on how to use an NEB method. + +The Initialization is : :: + + local image_label = "image_" + local n_images = 5 + local k_spring = 1 + local flos = require "flos" + local images = {} + + local read_geom = function(filename) + local file = io.open(filename, "r") + local na = tonumber(file:read()) + local R = flos.Array.zeros(na, 3) + file:read() + local i = 0 + local function tovector(s) + local t = {} + s:gsub('%S+', function(n) t[#t+1] = tonumber(n) end) + return t + end + for i = 1, na do + local line = file:read() + if line == nil then break end + -- Get stuff into the R + local v = tovector(line) + R[i][1] = v[1] + R[i][2] = v[2] + R[i][3] = v[3] + end + file:close() + return R + end + + for i = 0, n_images + 1 do + images[#images+1] = flos.MDStep{R=read_geom(image_label .. i .. ".xyz")} + end + + local NEB = flos.NEB(images,{k=k_spring}) + if siesta.IONode then + NEB:info() + end + n_images = nil + + local relax = {} + for i = 1, NEB.n_images do + relax[i] = {} + relax[i][1] = flos.CG{beta='PR',restart='Powell', line=flos.Line{optimizer = flos.LBFGS{H0 = 1. / 25.} } } + if siesta.IONode then + NEB:info() + end + + end + + local current_image = 1 + + local Unit = siesta.Units + +some user define functions: :: + + function siesta_update_DM(old, current) + + if not siesta.IONode then + return + end + local DM = label .. ".DM" + local old_DM = DM .. "." .. tostring(old) + local current_DM = DM .. "." .. tostring(current) + local initial_DM = DM .. ".0" + local final_DM = DM .. ".".. tostring(NEB.n_images+1) + print ("The Label of Old DM is : " .. old_DM) + print ("The Label of Current DM is : " .. current_DM) + if old==0 and current==0 then + print("Removing DM for Resuming") + IOprint("Deleting " .. DM .. " for a clean restart...") + os.execute("rm " .. DM) + end + + if 0 <= old and old <= NEB.n_images+1 and NEB:file_exists(DM) then + IOprint("Saving " .. DM .. " to " .. old_DM) + os.execute("mv " .. DM .. " " .. old_DM) + elseif NEB:file_exists(DM) then + IOprint("Deleting " .. DM .. " for a clean restart...") + os.execute("rm " .. DM) + end + + if NEB:file_exists(current_DM) then + IOprint("Deleting " .. DM .. " for a clean restart...") + os.execute("rm " .. DM) + IOprint("Restoring " .. current_DM .. " to " .. DM) + os.execute("cp " .. current_DM .. " " .. DM) + end + + end + + function siesta_update_xyz(current) + if not siesta.IONode then + return + end + local xyz_label = image_label ..tostring(current)..".xyz" + + local f=io.open(xyz_label,"w") + f:write(tostring(#NEB[current].R).."\n \n") + for i=1,#NEB[current].R do + f:write(string.format(" %19.17f",tostring(NEB[current].R[i][1])).. " "..string.format("%19.17f",tostring(NEB[current].R[i][2]))..string.format(" %19.17f",tostring(NEB[current].R[i][3])).."\n") + end + f:close() + -- + end + + +for the Move Part we have : :: + + function siesta_move(siesta) + + local fa = flos.Array.from(siesta.geom.fa) * Unit.Ang / Unit.eV + local E = siesta.E.total / Unit.eV + + NEB[current_image]:set{F=fa, E=E} + + if current_image == 0 then + current_image = NEB.n_images + 1 + siesta.geom.xa = NEB[current_image].R * Unit.Ang + + IOprint("\nLUA/NEB final state\n") + return {'geom.xa'} + + elseif current_image == NEB.n_images + 1 then + + current_image = 1 + + siesta.geom.xa = NEB[current_image].R * Unit.Ang + IOprint(("\nLUA/NEB running NEB image %d / %d\n"):format(current_image, NEB.n_images)) + return {'geom.xa'} + + elseif current_image < NEB.n_images then + current_image = current_image + 1 + siesta.geom.xa = NEB[current_image].R * Unit.Ang + IOprint(("\nLUA/NEB running NEB image %d / %d\n"):format(current_image, NEB.n_images)) + return {'geom.xa'} + end + + local relaxed = true + IOprint("\nNEB step") + local out_R = {} + for img = 1, NEB.n_images do + + local F = NEB:force(img, siesta.IONode) + IOprint("NEB: max F on image ".. img .. + (" = %10.5f, climbing = %s"):format(F:norm():max(), + tostring(NEB:climbing(img))) ) + local all_xa, weight = {}, flos.Array( #relax[img] ) + for i = 1, #relax[img] do + all_xa[i] = relax[img][i]:optimize(NEB[img].R, F) + weight[i] = relax[img][i].weight + end + weight = weight / weight:sum() + + if #relax[img] > 1 then + IOprint("\n weighted average for relaxation: ", tostring(weight)) + end + + local out_xa = all_xa[1] * weight[1] + relaxed = relaxed and relax[img][1]:optimized() + for i = 2, #relax[img] do + out_xa = out_xa + all_xa[i] * weight[i] + relaxed = relaxed and relax[img][i]:optimized() + end + + out_R[img] = out_xa + + end + + NEB:save( siesta.IONode ) + + for img = 1, NEB.n_images do + NEB[img]:set{R=out_R[img]} + end + current_image = 1 + if relaxed then + siesta.geom.xa = NEB.final.R * Unit.Ang + IOprint("\nLUA/NEB complete\n") + else + siesta.geom.xa = NEB[1].R * Unit.Ang + IOprint(("\nLUA/NEB running NEB image %d / %d\n"):format(current_image, NEB.n_images)) + end + + siesta.MD.Relaxed = relaxed + + return {"geom.xa", + "MD.Relaxed"} + end + +For our main siesta communicator function we have: :: + + function siesta_comm() + + local ret_tbl = {} + + if siesta.state == siesta.INITIALIZE then + siesta.receive({"Label", + "geom.xa", + "MD.MaxDispl", + "MD.MaxForceTol"}) + + label = tostring(siesta.Label) + IOprint("\nLUA NEB calculator") + + for img = 1, NEB.n_images do + IOprint(("\nLUA NEB relaxation method for image %d:"):format(img)) + for i = 1, #relax[img] do + relax[img][i].tolerance = siesta.MD.MaxForceTol * Unit.Ang / Unit.eV + relax[img][i].max_dF = siesta.MD.MaxDispl / Unit.Ang + if siesta.IONode then + relax[img][i]:info() + end + end + end + + siesta.geom.xa = NEB.initial.R * Unit.Ang + IOprint("\nLUA/NEB initial state\n") + current_image = 0 + siesta_update_DM(0, current_image) + siesta_update_xyz(current_image) + IOprint(NEB[current_image].R) + ret_tbl = {'geom.xa'} + end + + if siesta.state == siesta.MOVE then + + siesta.receive({"geom.fa", + "E.total", + "MD.Relaxed"}) + + local old_image = current_image + + ret_tbl = siesta_move(siesta) + + siesta_update_DM(old_image, current_image) + siesta_update_xyz(current_image) + IOprint(NEB[current_image].R) + + end + + siesta.send(ret_tbl) + end + + + +Double Nudged Elastic Band +.......................... + +For Using Double Nudged Elastic Band Only difference in Scripts is the initialization of DNEB object, The DNEB initialization is : :: + + local NEB = flos.DNEB(images,{k=k_spring}) + +Variable Cell Nudged Elastic Band +................................. + +Example on how to use an NEB method. + +The Initialization is : :: + + local flos = require "flos" + local image_label = "image_coordinates_" + local image_vector_label= "image_vectors_" + local n_images = 5 + local images = {} + local images_vectors={} + --local label = "MgO-3x3x1-2V" + local f_label_xyz = "image_coordinates_" + local f_label_xyz_vec = "image_vectors_" + local read_geom = function(filename) + local file = io.open(filename, "r") + local na = tonumber(file:read()) + local R = flos.Array.zeros(na, 3) + file:read() + local i = 0 + local function tovector(s) + local t = {} + s:gsub('%S+', function(n) t[#t+1] = tonumber(n) end) + return t + end + for i = 1, na do + + +Some user define functions: :: + + function stress_to_voigt(stress) + local voigt = flos.Array.empty(6) + voigt[1]=stress[1][1] + voigt[2]=stress[2][2] + voigt[3]=stress[3][3] + voigt[4]=(stress[2][3]+stress[3][2])*0.5 + voigt[5]=(stress[1][3]+stress[3][1])*0.5 + voigt[6]=(stress[1][2]+stress[2][1])*0.5 + return voigt + end + + function siesta_update_xyz(current) + if not siesta.IONode then + return + end + local xyz_label = f_label_xyz ..tostring(current)..".xyz" + + local f=io.open(xyz_label,"w") + f:write(tostring(#NEB[current].R).."\n \n") + for i=1,#NEB[current].R do + f:write(string.format(" %19.17f",tostring(NEB[current].R[i][1])).. " "..string.format("%19.17f",tostring(NEB[current].R[i][2]))..string.format(" %19.17f",tostring(NEB[current].R[i][3])).."\n") + end + f:close() + + end + + function siesta_update_xyz_vec(current) + if not siesta.IONode then + return + end + local xyz_vec_label = f_label_xyz_vec ..tostring(current)..".xyz" + local f=io.open(xyz_vec_label,"w") + f:write(tostring(#VCNEB[current].R).."\n \n") + for i=1,#VCNEB[current].R do + f:write(string.format(" %19.17f",tostring(VCNEB[current].R[i][1])).. " "..string.format("%19.17f",tostring(VCNEB[current].R[i][2]))..string.format(" %19.17f",tostring(VCNEB[current].R[i][3])).."\n") + end + f:close() + -- + end + + if not siesta.IONode then + return + end + local DM = label .. ".DM" + local old_DM = DM .. "." .. tostring(old) + local current_DM = DM .. "." .. tostring(current) + local initial_DM = DM .. ".0" + local final_DM = DM .. ".".. tostring(NEB.n_images+1) + print ("The Label of Old DM is : " .. old_DM) + print ("The Label of Current DM is : " .. current_DM) + if old==0 and current==0 then + print("Removing DM for Resuming") + IOprint("Deleting " .. DM .. " for a clean restart...") + os.execute("rm " .. DM) + end + + if 0 <= old and old <= NEB.n_images+1 and NEB:file_exists(DM) then + IOprint("Saving " .. DM .. " to " .. old_DM) + os.execute("mv " .. DM .. " " .. old_DM) + elseif NEB:file_exists(DM) then + IOprint("Deleting " .. DM .. " for a clean restart...") + os.execute("rm " .. DM) + end + + if NEB:file_exists(current_DM) then + IOprint("Deleting " .. DM .. " for a clean restart...") + os.execute("rm " .. DM) + IOprint("Restoring " .. current_DM .. " to " .. DM) + os.execute("cp " .. current_DM .. " " .. DM) + end + + end + + +For the Move Part we have : :: + + function siesta_move(siesta) + local fa = flos.Array.from(siesta.geom.fa) * Unit.Ang / Unit.eV + local E = siesta.E.total / Unit.eV + NEB[current_image]:set{F=fa, E=E} + local Vfa = (-flos.Array.from(siesta.geom.stress) * Unit.Ang ^ 3 / Unit.eV)--* vol + local VE = siesta.E.total / Unit.eV + VCNEB[current_image]:set{F=Vfa,E=VE} + if current_image == 0 then + current_image = NEB.n_images + 1 + siesta.geom.xa = NEB[current_image].R * Unit.Ang + siesta.geom.cell = VCNEB[current_image].R * Unit.Ang + IOprint("\nLUA/NEB final state\n") + IOprint("Lattice Vectors") + IOprint(VCNEB[current_image].R) + IOprint("Stresss") + IOprint(VCNEB[current_image].F) + return {'geom.xa',"geom.stress","geom.cell"} + elseif current_image == NEB.n_images + 1 then + current_image = 1 + siesta.geom.xa = NEB[current_image].R * Unit.Ang + siesta.geom.cell = VCNEB[current_image].R * Unit.Ang + IOprint(("\nLUA/NEB running NEB image %d / %d\n"):format(current_image, NEB.n_images)) + IOprint("Lattice Vectors") + IOprint(VCNEB[current_image].R) + IOprint("Stresss") + IOprint(VCNEB[current_image].F) + return {'geom.xa',"geom.stress","geom.cell"} + elseif current_image < NEB.n_images then + current_image = current_image + 1 + siesta.geom.xa = NEB[current_image].R * Unit.Ang + siesta.geom.cell = VCNEB[current_image].R * Unit.Ang + IOprint(("\nLUA/NEB running NEB image %d / %d\n"):format(current_image, NEB.n_images)) + IOprint("Lattice Vectors") + IOprint(VCNEB[current_image].R) + IOprint("Stresss") + IOprint(VCNEB[current_image].F) + return {'geom.xa',"geom.stress","geom.cell"} + end + local relaxed = true + local vcrelaxed = true + local tot_relax= false + IOprint("\nNEB step") + local out_R = {} + local out_VR = {} + for img = 1, NEB.n_images do + local F = NEB:force(img, siesta.IONode) + IOprint("NEB: max F on image ".. img .. + (" = %10.5f, climbing = %s"):format(F:norm():max(), + tostring(NEB:climbing(img))) ) + local all_xa, weight = {}, flos.Array( #relax[img] ) + for i = 1, #relax[img] do + all_xa[i] = relax[img][i]:optimize(NEB[img].R, F) + weight[i] = relax[img][i].weight + end + weight = weight / weight:sum() + if #relax[img] > 1 then + IOprint("\n weighted average for relaxation: ", tostring(weight)) + end + local out_xa = all_xa[1] * weight[1] + relaxed = relaxed and relax[img][1]:optimized() + for i = 2, #relax[img] do + out_xa = out_xa + all_xa[i] * weight[i] + relaxed = relaxed and relax[img][i]:optimized() + end + local icell = VCNEB[img].R --/ Unit.Ang + local ivol=icell[1]:cross(icell[2]):dot(icell[3]) + local strain=flos.Array.zeros(6) + local stress_mask=flos.Array.ones(6) + stress_mask[3]=0.0 + stress_mask[4]=0.0 + stress_mask[5]=0.0 + stress_mask[6]=0.0 + local stress=-stress_to_voigt(siesta.geom.stress)--* Unit.Ang ^ 3 / Unit.eV + stress = stress * stress_mask + local VF = VCNEB:force(img, siesta.IONode) + IOprint("VCNEB: max Strain F on image ".. img .. + (" = %10.5f, climbing = %s"):format(VF:norm():max(), + tostring(VCNEB:climbing(img))) ) + IOprint(VCNEB[img].F) + local all_vcxa, vcweight = {}, flos.Array( #vcrelax[img] ) + for i = 1, #vcrelax[img] do + all_vcxa[i] = vcrelax[img][i]:optimize(strain, stress )--* ivol + vcweight[i] = vcrelax[img][i].weight + end + vcweight = vcweight / vcweight:sum() + if #vcrelax[img] > 1 then + IOprint("\n weighted average for cell relaxation: ", tostring(vcweight)) + end + local out_vcxa = all_vcxa[1] * vcweight[1] + vcrelaxed = vcrelaxed and vcrelax[img][1]:optimized() + for i = 2, #relax[img] do + out_vcxa = out_vcxa + all_vcxa[i] * vcweight[i] + vcrelaxed = vcrelaxed and vcrelax[img][i]:optimized() + end + + all_vcxa = nil --all_strain = nil + strain = out_vcxa * stress_mask --strain = out_strain * stress_mask + out_vcxa = nil --strain = out_strain * stress_mask --out_strain = nil + local dcell = flos.Array(icell.shape) + dcell[1][1]=1.0 + strain[1] + dcell[1][2]=0.5 * strain[6] + dcell[1][3]=0.5 * strain[5] + dcell[2][1]=0.5 * strain[6] + dcell[2][2]=1.0 + strain[2] + dcell[2][3]=0.5 * strain[4] + dcell[3][1]=0.5 * strain[5] + dcell[3][2]=0.5 * strain[4] + dcell[3][3]=1.0 + strain[3] + local out_cell=icell:dot(dcell) + dcell = nil + local lat = flos.Lattice:new(icell) + local fxa = lat:fractional(out_xa) + xa =fxa:dot(out_cell) + lat = nil + fxa = nil + out_VR[img] = out_cell + out_R[img] = xa + end + + NEB:save( siesta.IONode ) + + for img = 1, NEB.n_images do + NEB[img]:set{R=out_R[img]} + VCNEB[img]:set{R=out_VR[img]} + end + current_image = 1 + if relaxed and vcrelaxed then + tot_relax= true + siesta.geom.xa = NEB.final.R * Unit.Ang + siesta.geom.cell = VCNEB.final.R * Unit.Ang + IOprint("\nLUA/NEB complete\n") + else + siesta.geom.xa = NEB[1].R * Unit.Ang + siesta.geom.cell = VCNEB[1].R * Unit.Ang + IOprint(("\nLUA/NEB running NEB image %d / %d\n"):format(current_image, NEB.n_images)) + IOprint("Lattice Vectors") + IOprint(VCNEB[1].R) + IOprint("Stresss") + IOprint(VCNEB[1].F) + end + siesta.MD.Relaxed = tot_relax + return {"geom.xa","geom.stress","geom.cell", + "MD.Relaxed"} + end + +For our main siesta communicator function we have: :: + + function siesta_comm() + local ret_tbl = {} + if siesta.state == siesta.INITIALIZE then + siesta.receive({"Label", + "geom.xa", + "MD.MaxDispl", + "MD.MaxForceTol", + "MD.MaxStressTol", + "geom.cell", + "geom.stress"}) + label = tostring(siesta.Label) + IOprint("\nLUA NEB calculator") + for img = 1, NEB.n_images do + IOprint(("\nLUA NEB relaxation method for image %d:"):format(img)) + for i = 1, #relax[img] do + relax[img][i].tolerance = siesta.MD.MaxForceTol * Unit.Ang / Unit.eV + relax[img][i].max_dF = siesta.MD.MaxDispl / Unit.Ang + vcrelax[img][i].tolerance = siesta.MD.MaxStressTol * Unit.Ang ^ 3 / Unit.eV + vcrelax[img][i].max_dF = siesta.MD.MaxDispl / Unit.Ang + if siesta.IONode then + relax[img][i]:info() + vcrelax[img][i]:info() + end + end + end + siesta.geom.xa = NEB.initial.R * Unit.Ang + siesta.geom.cell = VCNEB.initial.R * Unit.Ang + IOprint("\nLUA/NEB initial state\n") + current_image = 0 + siesta_update_DM(0, current_image) + siesta_update_xyz(current_image) + siesta_update_xyz_vec(current_image) + IOprint("============================================") + IOprint("Lattice Vector") + IOprint(VCNEB[current_image].R) + IOprint("============================================") + IOprint("Atomic Coordinates") + IOprint(NEB[current_image].R) + IOprint("============================================") + ret_tbl = {'geom.xa',"geom.stress","geom.cell"} + end + if siesta.state == siesta.MOVE then + siesta.receive({"geom.fa", + "E.total", + "MD.Relaxed", + "geom.cell", + "geom.stress"}) + local old_image = current_image + ret_tbl = siesta_move(siesta) + siesta_update_DM(old_image, current_image) + siesta_update_xyz(current_image) + siesta_update_xyz_vec(current_image) + end + siesta.send(ret_tbl) + end + + +Temperature Dependent Nudged Elastic Band +......................................... + +For Using Temperature Nudged Elastic Band Only difference in Scripts is the initialization of TNEB object with Temperature, The TNEB initialization is : :: + + local NEB = flos.TNEB(images,{k=k_spring},neb_temp=300) + +where the ``neb_temp`` is in ``K`` . + +Force Constants +--------------- + +This example reads the input options as read by +SIESTA and defines the FC type of run: + + - MD.FCFirst + - MD.FCLast + - MD.FCDispl (max-displacement, i.e. for the heaviest atom) + +This script will emulate the FC run built-in SIESTA and will only +create the DM file for the first (x0) coordinate. + +There are a couple of parameters: + + (1) same_displ = true|false + if true all displacements will be true, and the algorithm is equivalent + to the SIESTA FC run. + If false, the displacements are dependent on the relative masses of the + atomic species. The given displacement is then the maximum displacement, + i.e. the displacement on the heaviest atom. + + (2) displ = {} + a list of different displacements. If one is interested in several different + force constant runs with different displacements, this is a simple way + to do it all at once. + +The Initialization is : :: + + local same_displ = true + + local displ = {0.005, 0.01, 0.02, 0.03, 0.04} + local flos = require "flos" + local idispl = 1 + local FC = nil + local Unit = siesta.Units + +For the Move Part we have : :: + + function siesta_move(siesta) + + local fa = flos.Array.from(siesta.geom.fa) * Unit.Ang / Unit.eV + + siesta.geom.xa = FC:next(fa) * Unit.Ang + siesta.MD.Relaxed = FC:done() + + return {"geom.xa", + "MD.Relaxed"} + end + +For our main siesta communicator function we have: :: + + function siesta_comm() + + local ret_tbl = {} + if siesta.state == siesta.INITIALIZE then + siesta.receive({"geom.xa", + "geom.mass", + "MD.FC.Displ", + "MD.FC.First", + "MD.FC.Last"}) + + IOprint("\nLUA Using the FC run") + if displ == nil then + displ = { siesta.MD.FC.Displ / Unit.Ang } + end + + local xa = flos.Array.from(siesta.geom.xa) / Unit.Ang + indices = flos.Array.range(siesta.MD.FC.First, siesta.MD.FC.Last) + if same_displ then + FC = flos.ForceHessian(xa, indices, displ[idispl]) + else + FC = flos.ForceHessian(xa, indices, displ[idispl], + siesta.geom.mass) + end + + end + + if siesta.state == siesta.MOVE then + + siesta.receive({"geom.xa", + "geom.fa", + "Write.DM", + "Write.EndOfCycle.DM", + "MD.Relaxed"}) + + ret_tbl = siesta_move(siesta) + + siesta.Write.DM = false + ret_tbl[#ret_tbl+1] = "Write.DM" + siesta.Write.EndOfCycle.DM = false + ret_tbl[#ret_tbl+1] = "Write.EndOfCycle.DM" + + FC:save( ("FLOS.FC.%d"):format(idispl) ) + FC:save( ("FLOS.FCSYM.%d"):format(idispl), true ) + + if siesta.MD.Relaxed then + idispl = idispl + 1 + + if idispl <= #displ then + FC:reset() + FC:set_displacement(displ[idispl]) + siesta.geom.xa = FC:next() * Unit.Ang + siesta.MD.Relaxed = false + + end + + end + + end + + siesta.send(ret_tbl) + end + + diff --git a/Docs/source/index-backup.rst b/Docs/source/index-backup.rst new file mode 100644 index 0000000..7f43851 --- /dev/null +++ b/Docs/source/index-backup.rst @@ -0,0 +1,23 @@ +.. flos-documentation documentation master file, created by + sphinx-quickstart on Sun Jan 26 19:32:11 2020. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Welcome to flos-documentations! +============================================== +SIESTA (Spanish Initiative for Electronic Simulations with Thousands of Atoms) is one of the main ICN2's/ICMAB's simulation software. Co-authored by members of these labs, this package allows to run Densisty Functional Theory (DFT) calculations to simulate atomic-scale structures, molecules, materials, and nanodevices. This page is a technical guide on how to set up and run SIESTA-LUA on the HPCCM. It is not meant to describe the underlying theory: information about the mathematical and physical foundations of SIESTA can be found on the official documentation. By embedding Lua in existing fortran codes, one can exchange information from powerful DFT software “SIESTA” with scripting languages such as Lua. By abstracting the interface in fortran one can easily generalize a communication layer to facilitate on-the-fly interaction with the program. To do so we can compile the siesta with the fortran-Lua-hook library “flook”. Its main usage is the ability to change run-time variables at run-time in order to optimize, or even change, the execution path of the parent program. One of the library for which developed for siesta is the “flos” (flook+siesta). This library enables optimization schemes created in Lua to be used together with SIESTA via the flook library, hence the same flo+SIESTA=FLOS. This enables scripting level languages to inter-act and develop new MD schemes, such as new geometry constraints, geometry relaxations, Nudged Elastic Band (NEB),etc. + + + +.. toctree:: + :maxdepth: 2 + :caption: Contents: + + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` diff --git a/Docs/source/index.rst b/Docs/source/index.rst new file mode 100644 index 0000000..53df232 --- /dev/null +++ b/Docs/source/index.rst @@ -0,0 +1,23 @@ +.. flos-documentation documentation master file, created by + sphinx-quickstart on Sun Jan 26 19:32:11 2020. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Welcome to flos-documentations! +============================================== +SIESTA (Spanish Initiative for Electronic Simulations with Thousands of Atoms) is a DFT simulation software. This package allows to run Densisty Functional Theory (DFT) calculations to simulate atomic-scale structures, molecules, materials, and nanodevices. This page is a technical guide on how to set up and run SIESTA-LUA along with flos library. It is not meant to describe the underlying theory: information about the mathematical and physical foundations of SIESTA can be found on the official documentation. By embedding Lua in existing fortran codes, one can exchange information from powerful DFT software “SIESTA” with scripting languages such as Lua. By abstracting the interface in fortran one can easily generalize a communication layer to facilitate on-the-fly interaction with the program. To do so we can compile the siesta with the fortran-Lua-hook library “flook”. Its main usage is the ability to change run-time variables at run-time in order to optimize, or even change, the execution path of the parent program. One of the library for which developed for siesta is the “flos” (flook+siesta). This library enables optimization schemes created in Lua to be used together with SIESTA via the flook library, hence the same flo+SIESTA=FLOS. This enables scripting level languages to inter-act and develop new MD schemes, such as new geometry constraints, geometry relaxations, Nudged Elastic Band (NEB),etc. + + + +.. toctree:: + :maxdepth: 2 + :caption: Contents: + + 0-setting-up-flos + 1-some-basics + 2-tutorials + + +Indices and tables +================== + diff --git a/Docs/source/installation.rst b/Docs/source/installation.rst new file mode 100644 index 0000000..83260cd --- /dev/null +++ b/Docs/source/installation.rst @@ -0,0 +1 @@ +.. include:: ./content/installation.rst diff --git a/Utils/NEB/image_creator-v-0.4.py b/Utils/NEB/image_creator-v-0.4.py new file mode 100644 index 0000000..12b2d8f --- /dev/null +++ b/Utils/NEB/image_creator-v-0.4.py @@ -0,0 +1,198 @@ +# ========================================================================== +# Script for PDOS calculation +# Written by Arsalan Akhtar +# ICN2 26-September-2018-v-0.1 +# ICN2 04-February-2019-v-0.3 using ASE idpp path included to the script +# ICN2 25-February-2019-v-0.4 Parameters Added by Pol Febrer +# ========================================================================== +# Libray imports + +from ase import Atoms +from ase.neb import NEB +import os, shutil, sys +from linecache import getline +import numpy as np +import argparse + +#========================================================================== +# ----------------------USER Define parameters------------------------- +#========================================================================== + +#Parse all the arguments that we need +parser = argparse.ArgumentParser() +parser.add_argument('-d', "--directory", type=str, default=".", + help='Directory where the fdf files are located, default is the current directory') +parser.add_argument('-n', "--nimages", type=int, default=5, + help='Number of images that must be generated between the two states, default is 5') +parser.add_argument('-if', "--initialfile", type=str, default="initial", + help='Name of the initial structure file (without extension), default is "initial"') +parser.add_argument('-ff', "--finalfile", type=str, default="final", + help='Name of the final structure file (without extension), default is "final"') +parser.add_argument('-m', "--method", type=str, default="li", + help='Interpolation method to generate the images, default is linear interpolation (li), other options are: Image Dependent Pair Potential (idpp)') +args = parser.parse_args() + +#Get the working directory +wdir = args.directory + +#Get the arguments given (or the default ones) +NAME_OF_INITIAL_STRUCTURE_FILE = f"{wdir}/{args.initialfile}.fdf" +NAME_OF_FINAL_STRUCTURE_FILE = f"{wdir}/{args.finalfile}.fdf" +NUMBER_OF_IMAGES = args.nimages +Interpolation_method = args.method + +#========================================================================== +print ("*******************************************************************") +print ("This is script written by A.Akhtar for Generating IMAGES for NEB-LUA program") +print (f"Number of Images ={NUMBER_OF_IMAGES}") + +if Interpolation_method == "li": + print ("Linear Interpolation Method") +else: + print ("Image Dependent Pair Potential Method") + +print ("Email:arsalan.akhtar@icn2.cat") +print ("*******************************************************************") + +# ================================================= +# Function to read information from the .fdf files +# ================================================= + +def getInfoFromFdf(filename, labelOfFile = ""): + + chemSpec = [] + relax_info=[] + + listenForSpecies = False + listenForCoords = False + + for line in open(filename): + + #Remove comments + line = line.split("#")[0] + #Get the line in lowercase + lcLine = line.lower() + #Split the line + splitted = line.split() + + if 'systemlabel' in lcLine: + system_Label = splitted[-1] + + elif 'numberofspecies' in lcLine: + num_species = int(splitted[-1]) + + elif 'numberofatoms' in lcLine: + number_of_atoms = int(splitted[-1]) + + elif "chemicalspecieslabel" in lcLine: + listenForSpecies = not listenForSpecies + + elif listenForSpecies: + #Save atomic number and species (split by "." just in case there are suffixes, e.g. C.pbr) + chemSpec.append([int(splitted[1]),splitted[2].split(".")[0]]) + + elif "atomiccoordinatesandatomicspecies" in lcLine: + listenForCoords = not listenForCoords + + elif listenForCoords: + coords = [float(coord) for coord in splitted[:3]] + species = int(splitted[3]) #This is the index of the species, the name can be found with the help of chemSpec + relax_info.append([coords,species]) + + print ("(1) System label is : " + system_Label) + print ("(2) Number of Species are : " + str(num_species)) + print ("(3) Total Number of Atoms are : " + str(number_of_atoms)) + + #Convert the indexes saved in the relax_info to species names + relax_info = np.array(relax_info) + relax_info[:,1] = [chemSpec[specNum-1][1] for specNum in relax_info[:,1]] + + if len(relax_info) > 0: + print (f"{labelOfFile.upper()} COORDINATES READ\n") + else: + print(f"UNABLE TO READ {labelOfFile.upper()} COORDINATES\n") + + return [system_Label, num_species, number_of_atoms, np.array(chemSpec), relax_info] + +# ================================================================================== +# Opening NAME_OF_FINAL_STRUCTURE_FILE finding label, species and relaxed structure +# ================================================================================== + +print("READING INITIAL FILE...") + +[i_system_Label, i_num_species, +i_number_of_atoms, i_chemSpec, i_relax_info] = getInfoFromFdf(NAME_OF_INITIAL_STRUCTURE_FILE,"initial") + + +# ================================================================================== +# Opening NAME_OF_FINAL_STRUCTURE_FILE finding label, species and relaxed structure +# ================================================================================== + +print("READING FINAL FILE...") + +[f_system_Label, f_num_species, +f_number_of_atoms, f_chemSpec, f_relax_info] = getInfoFromFdf(NAME_OF_FINAL_STRUCTURE_FILE, "final") + +# ================================ +# Defining the structures for ase +# ================================ + +#Build the strings that Atoms() needs with the names of the species concatenated (e.g "CCHCCCHO") +specStrings = ["".join(i_relax_info[:,1]), "".join(f_relax_info[:,1])] + +#And then generate the initial and final images +initial = Atoms(specStrings[0], positions = list(i_relax_info[:,0])) +final = Atoms(specStrings[1], positions = list(f_relax_info[:,0])) + +# ==================================================== +# Creating a dummy path that ase needs to interpolate +# ==================================================== + +images = [initial] + +for i in range(NUMBER_OF_IMAGES): + images.append(initial.copy()) + +images.append(final) + +# ====================================== +# Interpolating the intermediate images +# ====================================== + +neb = NEB(images) +neb.interpolate(None if Interpolation_method == "li" else Interpolation_method) + +# ====================================== +# Writing the images to .xyz files +# ====================================== + +filename_anim = f"images_{Interpolation_method}_Animation.xyz" + +with open( f"{wdir}/{filename_anim}" , 'w') as f2: + + for i, image in enumerate(images): + + filename = f"images_{Interpolation_method}{i}.xyz" + + with open( f"{wdir}/{filename}" ,'w') as f1: + + f1.write(f"{i_number_of_atoms}\n") + f1.write(f"Image_{i}\n") + + for n in range(i_number_of_atoms): + + species = image.get_chemical_symbols()[n] + coords = "\t".join([ f"{coord:.8f}" for coord in image.get_positions()[n] ]) + + f1.write( f"{species}\t{coords}\n" ) + + with open( f"{wdir}/{filename}" , "r") as f1: + + f2.write(f1.read()) + + + + + + + diff --git a/examples/dneb_with_restart-new.lua b/examples/dneb_with_restart-new.lua new file mode 100644 index 0000000..4d96cd7 --- /dev/null +++ b/examples/dneb_with_restart-new.lua @@ -0,0 +1,344 @@ +--[[ +Example on how to use an NEB method. +--]] +--================================================================= +local image_label = "image_" +-- Total number of images (excluding initial[0] and final[n_images+1]) +local n_images = 5 +local k_spring = 1 +--================================================================= +-- Load the FLOS module +local flos = require "flos" +-- The prefix of the files that contain the images +-- Table of image geometries +local images = {} + +-- The default output label of the DM files +-- Function for reading a geometry +local read_geom = function(filename) + local file = io.open(filename, "r") + local na = tonumber(file:read()) + local R = flos.Array.zeros(na, 3) + file:read() + local i = 0 + local function tovector(s) + local t = {} + s:gsub('%S+', function(n) t[#t+1] = tonumber(n) end) + return t + end + for i = 1, na do + local line = file:read() + if line == nil then break end + -- Get stuff into the R + local v = tovector(line) + R[i][1] = v[1] + R[i][2] = v[2] + R[i][3] = v[3] + end + file:close() + return R +end + +-- Now read in the images +for i = 0, n_images + 1 do + images[#images+1] = flos.MDStep{R=read_geom(image_label .. i .. ".xyz")} +end + +-- Now we have all images... +local NEB = flos.DNEB(images,{k=k_spring}) +if siesta.IONode then + NEB:info() +end +-- Remove global (we use NEB.n_images) +n_images = nil + +-- Setup each image relaxation method (note it is prepared for several +-- relaxation methods per-image) +local relax = {} +for i = 1, NEB.n_images do + -- Select the relaxation method + relax[i] = {} + relax[i][1] = flos.CG{beta='PR',restart='Powell', line=flos.Line{optimizer = flos.LBFGS{H0 = 1. / 25.} } } + -- add more relaxation schemes if needed ;) + --relax[i][2] = flos.CG{beta='PR',restart='Powell', line=flos.Line{optimizer = flos.LBFGS{H0 = 1. / 50.} } } + --relax[i][3] = flos.CG{beta='PR',restart='Powell', line=flos.Line{optimizer = flos.LBFGS{H0 = 1. / 75.} } } + --relax[i][4] = flos.LBFGS{H0 = 1. / 50} + --relax[i][5] = flos.FIRE{dt_init = 1., direction="global", correct="global"} + if siesta.IONode then + NEB:info() + end + +end + +-- Counter for controlling which image we are currently relaxing +local current_image = 1 + +-- Grab the unit table of siesta (it is already created +-- by SIESTA) +local Unit = siesta.Units + + +function siesta_comm() + + -- This routine does exchange of data with SIESTA + local ret_tbl = {} + + -- Do the actual communication with SIESTA + if siesta.state == siesta.INITIALIZE then + + -- In the initialization step we request the + -- convergence criteria + -- MD.MaxDispl + -- MD.MaxForceTol + siesta.receive({"Label", + "geom.xa", + "MD.MaxDispl", + "MD.MaxForceTol"}) + + -- Store the Label + label = tostring(siesta.Label) + + -- Print information + IOprint("\nLUA NEB calculator") + + -- Ensure we update the convergence criteria + -- from SIESTA (in this way one can ensure siesta options) + for img = 1, NEB.n_images do + IOprint(("\nLUA NEB relaxation method for image %d:"):format(img)) + for i = 1, #relax[img] do + relax[img][i].tolerance = siesta.MD.MaxForceTol * Unit.Ang / Unit.eV + relax[img][i].max_dF = siesta.MD.MaxDispl / Unit.Ang + + -- Print information for this relaxation method + if siesta.IONode then + relax[img][i]:info() + end + end + end + + -- This is only reached one time, and that it as the beginning... + -- be sure to set the corresponding values + siesta.geom.xa = NEB.initial.R * Unit.Ang + + IOprint("\nLUA/NEB initial state\n") + -- force the initial image to be the first one to run + current_image = 0 + siesta_update_DM(0, current_image) + --Write xyz File + siesta_update_xyz(current_image) + IOprint(NEB[current_image].R) + + ret_tbl = {'geom.xa'} + + end + + if siesta.state == siesta.MOVE then + + -- Here we are doing the actual LBFGS algorithm. + -- We retrieve the current coordinates, the forces + -- and whether the geometry has relaxed + siesta.receive({"geom.fa", + "E.total", + "MD.Relaxed"}) + + -- Store the old image that has been tested, + -- in this way we can check whether we have moved to + -- a new image. + local old_image = current_image + + ret_tbl = siesta_move(siesta) + + -- we need to re-organize the DM files for faster convergence + -- pass whether the image is the same + siesta_update_DM(old_image, current_image) + siesta_update_xyz(current_image) + IOprint(NEB[current_image].R) + + end + + siesta.send(ret_tbl) +end + +function siesta_move(siesta) + + -- Retrieve the atomic coordinates, forces and the energy + local fa = flos.Array.from(siesta.geom.fa) * Unit.Ang / Unit.eV + local E = siesta.E.total / Unit.eV + + -- First update the coordinates, forces and energy for the + -- just calculated image + NEB[current_image]:set{F=fa, E=E} + + if current_image == 0 then + -- Perform the final image, to retain that information + current_image = NEB.n_images + 1 + + -- Set the atomic coordinates for the final image + siesta.geom.xa = NEB[current_image].R * Unit.Ang + + IOprint("\nLUA/NEB final state\n") + --siesta_update_DM(0, current_image) + -- The siesta relaxation is already not set + return {'geom.xa'} + + elseif current_image == NEB.n_images + 1 then + + -- Start the NEB calculation + current_image = 1 + + -- Set the atomic coordinates for the final image + siesta.geom.xa = NEB[current_image].R * Unit.Ang + + IOprint(("\nLUA/NEB running NEB image %d / %d\n"):format(current_image, NEB.n_images)) + + -- The siesta relaxation is already not set + return {'geom.xa'} + + elseif current_image < NEB.n_images then + + current_image = current_image + 1 + + -- Set the atomic coordinates for the image + siesta.geom.xa = NEB[current_image].R * Unit.Ang + + IOprint(("\nLUA/NEB running NEB image %d / %d\n"):format(current_image, NEB.n_images)) + + -- The siesta relaxation is already not set + return {'geom.xa'} + + end + + -- First we figure out how perform the NEB optimizations + -- Now we have calculated all the systems and are ready for doing + -- an NEB MD step + + -- Global variable to check for the NEB convergence + -- Initially assume it has relaxed + local relaxed = true + + IOprint("\nNEB step") + local out_R = {} + + -- loop on all images and pass the updated forces to the mixing algorithm + for img = 1, NEB.n_images do + + -- Get the correct NEB force (note that the relaxation + -- methods require the negative force) + local F = NEB:force(img, siesta.IONode) + IOprint("NEB: max F on image ".. img .. + (" = %10.5f, climbing = %s"):format(F:norm():max(), + tostring(NEB:climbing(img))) ) + + -- Prepare the relaxation for image `img` + local all_xa, weight = {}, flos.Array( #relax[img] ) + for i = 1, #relax[img] do + all_xa[i] = relax[img][i]:optimize(NEB[img].R, F) + weight[i] = relax[img][i].weight + end + weight = weight / weight:sum() + + if #relax[img] > 1 then + IOprint("\n weighted average for relaxation: ", tostring(weight)) + end + + -- Calculate the new coordinates and figure out + -- if the algorithm has converged (all forces below) + local out_xa = all_xa[1] * weight[1] + relaxed = relaxed and relax[img][1]:optimized() + for i = 2, #relax[img] do + out_xa = out_xa + all_xa[i] * weight[i] + relaxed = relaxed and relax[img][i]:optimized() + end + + -- Copy the optimized coordinates to a table + out_R[img] = out_xa + + end + + -- Before we update the coordinates we will write + -- the current steps results to the result file + -- (this HAS to be done before updating the coordinates) + NEB:save( siesta.IONode ) + + -- Now we may copy over the coordinates (otherwise + -- we do a consecutive update, and then overwrite) + for img = 1, NEB.n_images do + NEB[img]:set{R=out_R[img]} + end + + -- Start over in case the system has not relaxed + current_image = 1 + if relaxed then + -- the final coordinates are returned + siesta.geom.xa = NEB.final.R * Unit.Ang + IOprint("\nLUA/NEB complete\n") + else + siesta.geom.xa = NEB[1].R * Unit.Ang + IOprint(("\nLUA/NEB running NEB image %d / %d\n"):format(current_image, NEB.n_images)) + end + + siesta.MD.Relaxed = relaxed + + return {"geom.xa", + "MD.Relaxed"} +end + +-- Function for retaining the DM files for the images so that we +-- can easily restart etc. +function siesta_update_DM(old, current) + + if not siesta.IONode then + -- only allow the IOnode to perform stuff... + return + end + -- Move about files so that we re-use old DM files + local DM = label .. ".DM" + local old_DM = DM .. "." .. tostring(old) + local current_DM = DM .. "." .. tostring(current) + local initial_DM = DM .. ".0" + local final_DM = DM .. ".".. tostring(NEB.n_images+1) + print ("The Label of Old DM is : " .. old_DM) + print ("The Label of Current DM is : " .. current_DM) + -- Saving initial DM + if old==0 and current==0 then + print("Removing DM for Resuming") + IOprint("Deleting " .. DM .. " for a clean restart...") + os.execute("rm " .. DM) + end + + if 0 <= old and old <= NEB.n_images+1 and NEB:file_exists(DM) then + -- store the current DM for restart purposes + IOprint("Saving " .. DM .. " to " .. old_DM) + os.execute("mv " .. DM .. " " .. old_DM) + elseif NEB:file_exists(DM) then + IOprint("Deleting " .. DM .. " for a clean restart...") + os.execute("rm " .. DM) + end + + if NEB:file_exists(current_DM) then + IOprint("Deleting " .. DM .. " for a clean restart...") + os.execute("rm " .. DM) + IOprint("Restoring " .. current_DM .. " to " .. DM) + os.execute("cp " .. current_DM .. " " .. DM) + end + +end + +function siesta_update_xyz(current) + if not siesta.IONode then + -- only allow the IOnode to perform stuff... + return + end + local xyz_label = image_label ..tostring(current)..".xyz" + --self:_n_images=self.n_images + --self:_check_image(image) + + local f=io.open(xyz_label,"w") + f:write(tostring(#NEB[current].R).."\n \n") + --f:write(tostring(initialize:self.n_images).."\n \n") + for i=1,#NEB[current].R do + f:write(string.format(" %19.17f",tostring(NEB[current].R[i][1])).. " "..string.format("%19.17f",tostring(NEB[current].R[i][2]))..string.format(" %19.17f",tostring(NEB[current].R[i][3])).."\n") + end + f:close() + -- +end diff --git a/examples/neb_analysis.lua b/examples/neb_analysis.lua new file mode 100644 index 0000000..1d0be49 --- /dev/null +++ b/examples/neb_analysis.lua @@ -0,0 +1,209 @@ +--[[ +Example on how to use an NEB Analysis. +--]] +--=================================================== +-- USER Define Vaiables +-- The prefix of the files that contain the images +local image_label = "image_" +local image_number = 3 +local cleanup ="yes" +--=================================================== +-- Load the FLOS module +local flos = require "flos" +-- Table of image geometries +local images = {} +-- The default output label of the DM files + +-- Function for reading a geometry +local read_geom = function(filename) + local file = io.open(filename, "r") + local na = tonumber(file:read()) + local R = flos.Array.zeros(na, 3) + file:read() + local i = 0 + local function tovector(s) + local t = {} + s:gsub('%S+', function(n) t[#t+1] = tonumber(n) end) + return t + end + for i = 1, na do + local line = file:read() + if line == nil then break end + -- Get stuff into the R + local v = tovector(line) + R[i][1] = v[1] + R[i][2] = v[2] + R[i][3] = v[3] + end + file:close() + return R +end + +-- Now read in the images +images[1]= flos.MDStep{R=read_geom(image_label .. image_number .. ".xyz")} +-- Grab the unit table of siesta (it is already created +-- by SIESTA) +local Unit = siesta.Units + + +function siesta_comm() + -- This routine does exchange of data with SIESTA + --local ret_tbl = {} + -- Do the actual communication with SIESTA + if siesta.state == siesta.INITIALIZE then --INITIALIZE + siesta.receive({"Label","geom.xa","MD.Relaxed"}) + --siesta.receive({"MD.Relaxed"}) + --Store the Label + label = tostring(siesta.Label) + -- Print information + siesta_update_DM(image_number) + IOprint("\nLUA NEB Analysis for image :".. image_label .. "calculator") + -- This is only reached one time, and that it as the beginning... + -- be sure to set the corresponding values + siesta.geom.xa = images[1].R* Unit.Ang --NEB.initial.R * Unit.Ang + siesta.send({"geom.xa"}) + IOprint("\nLUA NEB Analysis for image Coordinates :\n") + IOprint(images[1].R* Unit.Ang ) + + end + + if siesta.state == siesta.MOVE then + -- Here we are doing the actual LBFGS algorithm. + -- We retrieve the current coordinates, the forces + -- and whether the geometry has relaxed + siesta.receive({"MD.Relaxed"}) + IOprint("\nLUA/NEB MOVE state STARTED\n") + siesta.MD.Relaxed = true + siesta.send({"MD.Relaxed"}) + end + + if siesta.state == siesta.ANALYSIS_AFTER then + IOprint("\nLUA/NEB AFTER ANALYSIS state STARTED\n") + siesta_update_Analysis(image_number) + --os.execute("cp " .. label .. ".PDOS" .. " " .. label .. ".PDOS.3") + -- IOprint("\nLUA/NEB MOVE state FINISHED\n") + + siesta_cleanup(cleanup) + --ret_tbl = siesta_move(siesta) + end + +end + +function siesta_update_DM(image_number) + + if not siesta.IONode then + -- only allow the IOnode to perform stuff... + return + end + -- Move about files so that we re-use old DM files + local DM = label .. ".DM" + local current_DM = DM .. "." .. tostring(image_number) + -- Saving initial DM + IOprint("Saving " .. current_DM .. " to " .. DM) + os.execute("cp " .. current_DM .. " " .. DM) + +end + +function siesta_update_Analysis(image_number) + + if not siesta.IONode then + -- only allow the IOnode to perform stuff... + return + end + -- Move about files so that we re-use old DM files + local PDOS = label .. ".PDOS" + local DOS = label .. ".DOS" + local EIG = label .. ".EIG" + local BAND = label .. ".bands" + local FA = label .. ".FA" + local FAC = label .. ".FAC" + local PDOSKP = label .. ".PDOS.KP" + local PDOSxml = label .. ".PDOS.xml" + local XV = label .. ".XV" + local XYZ = label .. ".xyz" + local FORCE_STRESS = "FORCE_STRESS" + local current_PDOS = PDOS .. "." .. tostring(image_number) + local current_DOS = DOS .. "." .. tostring(image_number) + local current_EIG = EIG .. "." .. tostring(image_number) + local current_BAND = BAND .. "." .. tostring(image_number) + local current_FA = FA .. "." .. tostring(image_number) + local current_FAC = FAC .. "." .. tostring(image_number) + local current_PDOSKP = PDOSKP .. "." .. tostring(image_number) + local current_PDOSxml = PDOSxml .. "." .. tostring(image_number) + local current_FORCE_STRESS = FORCE_STRESS .. "." .. tostring(image_number) + local current_XV = XV .. "." .. tostring(image_number) + local current_XYZ = XYZ .. "." .. tostring(image_number) + -- Saving initial PDOS + IOprint("Saving " .. PDOS .. " to " .. current_PDOS) + os.execute("mv " .. PDOS .. " " .. current_PDOS) + -- Saving initial DOS + IOprint("Saving " .. DOS .. " to " .. current_DOS) + os.execute("mv " .. DOS .. " " .. current_DOS) + -- Saving initial EIG + IOprint("Saving " .. EIG .. " to " .. current_EIG) + os.execute("mv " .. EIG .. " " .. current_EIG) + -- Saving initial BAND + IOprint("Saving " .. BAND .. " to " .. current_BAND) + os.execute("mv " .. BAND .. " " .. current_BAND) + -- Saving initial FA + IOprint("Saving " .. FA .. " to " .. current_FA) + os.execute("mv " .. FA .. " " .. current_FA) + -- Saving initial FAC + IOprint("Saving " .. FAC .. " to " .. current_FAC) + os.execute("mv " .. FAC .. " " .. current_FAC) + -- Saving initial PDOSKP + IOprint("Saving " .. PDOSKP .. " to " .. current_PDOSKP) + os.execute("mv " .. PDOSKP .. " " .. current_PDOSKP) + -- Saving initial PDOSxml + IOprint("Saving " .. PDOSxml .. " to " .. current_PDOSxml) + os.execute("mv " .. PDOSxml .. " " .. current_PDOSxml) + -- Saving initial XV + IOprint("Saving " .. XV .. " to " .. current_XV) + os.execute("mv " .. XV .. " " .. current_XV) + -- Saving initial xyz + IOprint("Saving " .. XYZ .. " to " .. current_XYZ) + os.execute("mv " .. XYZ .. " " .. current_XYZ) + + -- Saving initial FORCE_STRESS + IOprint("Saving " .. FORCE_STRESS .. " to " .. current_FORCE_STRESS) + os.execute("mv " .. FORCE_STRESS .. " " .. current_FORCE_STRESS) + +end + +function siesta_cleanup(yes) + + if not siesta.IONode then + -- only allow the IOnode to perform stuff... + return + end + -- Move about files so that we re-use old DM files + -- Saving initial PDOS + --IOprint("Saving " .. PDOS .. " to " .. current_PDOS) + if yes=="yes" then + IOprint("These Files Ghoing to be Deleted :\n") + IOprint("BASIS_ENTHALPY\n" .. + "chlocal.charge\n" .. + "PARALLEL_DIST\n".. + "NON_TRIMMED_KP_LIST\n".. + "*.log\n" .. + "CHLOCAL.*\n".. + "*.BONDS* \n".. + "INPUT_TMP.* \n".. + "ORB.* \n".. + "SPLIT_SCAN*\n".. + "RED_VLOCAL.* \n".. + "*.Vxc* \n".. + "*.Vhart*\n" .. + "*.psdump\n" .. + "*.ion.*\n" .. + "VNA.*\n" .. + "*.confpot\n" .. + "*.charge\n" .. + "KB.*\n".. + "*STRUCT_OUT*\n".. + "*.Vsoft\n" + ) + os.execute("rm BASIS_ENTHALPY BASIS_HARRIS_ENTHALPY chlocal.charge PARALLEL_DIST NON_TRIMMED_KP_LIST ") + os.execute("rm *.log CHLOCAL.* *.BONDS* INPUT_TMP.* ORB.* SPLIT_SCAN* RED_VLOCAL.* *.Vxc* *.Vhart* *.psdump *.ion.* VNA.* *.confpot *.charge KB.* *STRUCT_OUT* *.Vsoft " ) + end +end diff --git a/examples/neb_with_restart-new.lua b/examples/neb_with_restart-new.lua new file mode 100644 index 0000000..f3e1376 --- /dev/null +++ b/examples/neb_with_restart-new.lua @@ -0,0 +1,344 @@ +--[[ +Example on how to use an NEB method. +--]] +--================================================================= +local image_label = "image_" +-- Total number of images (excluding initial[0] and final[n_images+1]) +local n_images = 5 +local k_spring = 1 +--================================================================= +-- Load the FLOS module +local flos = require "flos" +-- The prefix of the files that contain the images +-- Table of image geometries +local images = {} + +-- The default output label of the DM files +-- Function for reading a geometry +local read_geom = function(filename) + local file = io.open(filename, "r") + local na = tonumber(file:read()) + local R = flos.Array.zeros(na, 3) + file:read() + local i = 0 + local function tovector(s) + local t = {} + s:gsub('%S+', function(n) t[#t+1] = tonumber(n) end) + return t + end + for i = 1, na do + local line = file:read() + if line == nil then break end + -- Get stuff into the R + local v = tovector(line) + R[i][1] = v[1] + R[i][2] = v[2] + R[i][3] = v[3] + end + file:close() + return R +end + +-- Now read in the images +for i = 0, n_images + 1 do + images[#images+1] = flos.MDStep{R=read_geom(image_label .. i .. ".xyz")} +end + +-- Now we have all images... +local NEB = flos.NEB(images,{k=k_spring}) +if siesta.IONode then + NEB:info() +end +-- Remove global (we use NEB.n_images) +n_images = nil + +-- Setup each image relaxation method (note it is prepared for several +-- relaxation methods per-image) +local relax = {} +for i = 1, NEB.n_images do + -- Select the relaxation method + relax[i] = {} + relax[i][1] = flos.CG{beta='PR',restart='Powell', line=flos.Line{optimizer = flos.LBFGS{H0 = 1. / 25.} } } + -- add more relaxation schemes if needed ;) + --relax[i][2] = flos.CG{beta='PR',restart='Powell', line=flos.Line{optimizer = flos.LBFGS{H0 = 1. / 50.} } } + --relax[i][3] = flos.CG{beta='PR',restart='Powell', line=flos.Line{optimizer = flos.LBFGS{H0 = 1. / 75.} } } + --relax[i][4] = flos.LBFGS{H0 = 1. / 50} + --relax[i][5] = flos.FIRE{dt_init = 1., direction="global", correct="global"} + if siesta.IONode then + NEB:info() + end + +end + +-- Counter for controlling which image we are currently relaxing +local current_image = 1 + +-- Grab the unit table of siesta (it is already created +-- by SIESTA) +local Unit = siesta.Units + + +function siesta_comm() + + -- This routine does exchange of data with SIESTA + local ret_tbl = {} + + -- Do the actual communication with SIESTA + if siesta.state == siesta.INITIALIZE then + + -- In the initialization step we request the + -- convergence criteria + -- MD.MaxDispl + -- MD.MaxForceTol + siesta.receive({"Label", + "geom.xa", + "MD.MaxDispl", + "MD.MaxForceTol"}) + + -- Store the Label + label = tostring(siesta.Label) + + -- Print information + IOprint("\nLUA NEB calculator") + + -- Ensure we update the convergence criteria + -- from SIESTA (in this way one can ensure siesta options) + for img = 1, NEB.n_images do + IOprint(("\nLUA NEB relaxation method for image %d:"):format(img)) + for i = 1, #relax[img] do + relax[img][i].tolerance = siesta.MD.MaxForceTol * Unit.Ang / Unit.eV + relax[img][i].max_dF = siesta.MD.MaxDispl / Unit.Ang + + -- Print information for this relaxation method + if siesta.IONode then + relax[img][i]:info() + end + end + end + + -- This is only reached one time, and that it as the beginning... + -- be sure to set the corresponding values + siesta.geom.xa = NEB.initial.R * Unit.Ang + + IOprint("\nLUA/NEB initial state\n") + -- force the initial image to be the first one to run + current_image = 0 + siesta_update_DM(0, current_image) + --Write xyz File + siesta_update_xyz(current_image) + IOprint(NEB[current_image].R) + + ret_tbl = {'geom.xa'} + + end + + if siesta.state == siesta.MOVE then + + -- Here we are doing the actual LBFGS algorithm. + -- We retrieve the current coordinates, the forces + -- and whether the geometry has relaxed + siesta.receive({"geom.fa", + "E.total", + "MD.Relaxed"}) + + -- Store the old image that has been tested, + -- in this way we can check whether we have moved to + -- a new image. + local old_image = current_image + + ret_tbl = siesta_move(siesta) + + -- we need to re-organize the DM files for faster convergence + -- pass whether the image is the same + siesta_update_DM(old_image, current_image) + siesta_update_xyz(current_image) + IOprint(NEB[current_image].R) + + end + + siesta.send(ret_tbl) +end + +function siesta_move(siesta) + + -- Retrieve the atomic coordinates, forces and the energy + local fa = flos.Array.from(siesta.geom.fa) * Unit.Ang / Unit.eV + local E = siesta.E.total / Unit.eV + + -- First update the coordinates, forces and energy for the + -- just calculated image + NEB[current_image]:set{F=fa, E=E} + + if current_image == 0 then + -- Perform the final image, to retain that information + current_image = NEB.n_images + 1 + + -- Set the atomic coordinates for the final image + siesta.geom.xa = NEB[current_image].R * Unit.Ang + + IOprint("\nLUA/NEB final state\n") + --siesta_update_DM(0, current_image) + -- The siesta relaxation is already not set + return {'geom.xa'} + + elseif current_image == NEB.n_images + 1 then + + -- Start the NEB calculation + current_image = 1 + + -- Set the atomic coordinates for the final image + siesta.geom.xa = NEB[current_image].R * Unit.Ang + + IOprint(("\nLUA/NEB running NEB image %d / %d\n"):format(current_image, NEB.n_images)) + + -- The siesta relaxation is already not set + return {'geom.xa'} + + elseif current_image < NEB.n_images then + + current_image = current_image + 1 + + -- Set the atomic coordinates for the image + siesta.geom.xa = NEB[current_image].R * Unit.Ang + + IOprint(("\nLUA/NEB running NEB image %d / %d\n"):format(current_image, NEB.n_images)) + + -- The siesta relaxation is already not set + return {'geom.xa'} + + end + + -- First we figure out how perform the NEB optimizations + -- Now we have calculated all the systems and are ready for doing + -- an NEB MD step + + -- Global variable to check for the NEB convergence + -- Initially assume it has relaxed + local relaxed = true + + IOprint("\nNEB step") + local out_R = {} + + -- loop on all images and pass the updated forces to the mixing algorithm + for img = 1, NEB.n_images do + + -- Get the correct NEB force (note that the relaxation + -- methods require the negative force) + local F = NEB:force(img, siesta.IONode) + IOprint("NEB: max F on image ".. img .. + (" = %10.5f, climbing = %s"):format(F:norm():max(), + tostring(NEB:climbing(img))) ) + + -- Prepare the relaxation for image `img` + local all_xa, weight = {}, flos.Array( #relax[img] ) + for i = 1, #relax[img] do + all_xa[i] = relax[img][i]:optimize(NEB[img].R, F) + weight[i] = relax[img][i].weight + end + weight = weight / weight:sum() + + if #relax[img] > 1 then + IOprint("\n weighted average for relaxation: ", tostring(weight)) + end + + -- Calculate the new coordinates and figure out + -- if the algorithm has converged (all forces below) + local out_xa = all_xa[1] * weight[1] + relaxed = relaxed and relax[img][1]:optimized() + for i = 2, #relax[img] do + out_xa = out_xa + all_xa[i] * weight[i] + relaxed = relaxed and relax[img][i]:optimized() + end + + -- Copy the optimized coordinates to a table + out_R[img] = out_xa + + end + + -- Before we update the coordinates we will write + -- the current steps results to the result file + -- (this HAS to be done before updating the coordinates) + NEB:save( siesta.IONode ) + + -- Now we may copy over the coordinates (otherwise + -- we do a consecutive update, and then overwrite) + for img = 1, NEB.n_images do + NEB[img]:set{R=out_R[img]} + end + + -- Start over in case the system has not relaxed + current_image = 1 + if relaxed then + -- the final coordinates are returned + siesta.geom.xa = NEB.final.R * Unit.Ang + IOprint("\nLUA/NEB complete\n") + else + siesta.geom.xa = NEB[1].R * Unit.Ang + IOprint(("\nLUA/NEB running NEB image %d / %d\n"):format(current_image, NEB.n_images)) + end + + siesta.MD.Relaxed = relaxed + + return {"geom.xa", + "MD.Relaxed"} +end + +-- Function for retaining the DM files for the images so that we +-- can easily restart etc. +function siesta_update_DM(old, current) + + if not siesta.IONode then + -- only allow the IOnode to perform stuff... + return + end + -- Move about files so that we re-use old DM files + local DM = label .. ".DM" + local old_DM = DM .. "." .. tostring(old) + local current_DM = DM .. "." .. tostring(current) + local initial_DM = DM .. ".0" + local final_DM = DM .. ".".. tostring(NEB.n_images+1) + print ("The Label of Old DM is : " .. old_DM) + print ("The Label of Current DM is : " .. current_DM) + -- Saving initial DM + if old==0 and current==0 then + print("Removing DM for Resuming") + IOprint("Deleting " .. DM .. " for a clean restart...") + os.execute("rm " .. DM) + end + + if 0 <= old and old <= NEB.n_images+1 and NEB:file_exists(DM) then + -- store the current DM for restart purposes + IOprint("Saving " .. DM .. " to " .. old_DM) + os.execute("mv " .. DM .. " " .. old_DM) + elseif NEB:file_exists(DM) then + IOprint("Deleting " .. DM .. " for a clean restart...") + os.execute("rm " .. DM) + end + + if NEB:file_exists(current_DM) then + IOprint("Deleting " .. DM .. " for a clean restart...") + os.execute("rm " .. DM) + IOprint("Restoring " .. current_DM .. " to " .. DM) + os.execute("cp " .. current_DM .. " " .. DM) + end + +end + +function siesta_update_xyz(current) + if not siesta.IONode then + -- only allow the IOnode to perform stuff... + return + end + local xyz_label = image_label ..tostring(current)..".xyz" + --self:_n_images=self.n_images + --self:_check_image(image) + + local f=io.open(xyz_label,"w") + f:write(tostring(#NEB[current].R).."\n \n") + --f:write(tostring(initialize:self.n_images).."\n \n") + for i=1,#NEB[current].R do + f:write(string.format(" %19.17f",tostring(NEB[current].R[i][1])).. " "..string.format("%19.17f",tostring(NEB[current].R[i][2]))..string.format(" %19.17f",tostring(NEB[current].R[i][3])).."\n") + end + f:close() + -- +end diff --git a/examples/neb_with_restart.lua b/examples/neb_with_restart.lua new file mode 100644 index 0000000..c81cfed --- /dev/null +++ b/examples/neb_with_restart.lua @@ -0,0 +1,347 @@ +--[[ +Example on how to use an NEB method. +--]] + +-- Load the FLOS module +local flos = require "flos" + +-- The prefix of the files that contain the images +local image_label = "images_" + +-- Total number of images (excluding initial[0] and final[n_images+1]) +local n_images = 5 +-- Table of image geometries +local images = {} + +-- The default output label of the DM files +local label = "MgO-3x3x1-2V" +local f_label_xyz= "images_" +-- Function for reading a geometry +local read_geom = function(filename) + local file = io.open(filename, "r") + local na = tonumber(file:read()) + local R = flos.Array.zeros(na, 3) + file:read() + local i = 0 + local function tovector(s) + local t = {} + s:gsub('%S+', function(n) t[#t+1] = tonumber(n) end) + return t + end + for i = 1, na do + local line = file:read() + if line == nil then break end + -- Get stuff into the R + local v = tovector(line) + R[i][1] = v[1] + R[i][2] = v[2] + R[i][3] = v[3] + end + file:close() + return R +end + +-- Now read in the images +for i = 0, n_images + 1 do + images[#images+1] = flos.MDStep{R=read_geom(image_label .. i .. ".xyz")} +end + +-- Now we have all images... +local NEB = flos.NEB(images) +NEB.DM_label="MgO-3x3x1-2V" +if siesta.IONode then + NEB:info() +end +-- Remove global (we use NEB.n_images) +n_images = nil + +-- Setup each image relaxation method (note it is prepared for several +-- relaxation methods per-image) +local relax = {} +for i = 1, NEB.n_images do + -- Select the relaxation method + relax[i] = {} + relax[i][1] = flos.CG{beta='PR',restart='Powell', line=flos.Line{optimizer = flos.LBFGS{H0 = 1. / 25.} } } + relax[i][2] = flos.CG{beta='PR',restart='Powell', line=flos.Line{optimizer = flos.LBFGS{H0 = 1. / 50.} } } + relax[i][3] = flos.CG{beta='PR',restart='Powell', line=flos.Line{optimizer = flos.LBFGS{H0 = 1. / 75.} } } + if siesta.IONode then + NEB:info() + end + --relax[i][2] = flos.LBFGS{H0 = 1. / 50} + + --relax[i][1] = flos.FIRE{dt_init = 1., direction="global", correct="global"} + -- add more relaxation schemes if needed ;) +end + +-- Counter for controlling which image we are currently relaxing +local current_image = 1 + +-- Grab the unit table of siesta (it is already created +-- by SIESTA) +local Unit = siesta.Units + + +function siesta_comm() + + -- This routine does exchange of data with SIESTA + local ret_tbl = {} + + -- Do the actual communication with SIESTA + if siesta.state == siesta.INITIALIZE then + + -- In the initialization step we request the + -- convergence criteria + -- MD.MaxDispl + -- MD.MaxForceTol + siesta.receive({"Label", + "geom.xa", + "MD.MaxDispl", + "MD.MaxForceTol"}) + + -- Store the Label + label = tostring(siesta.Label) + + -- Print information + IOprint("\nLUA NEB calculator") + + -- Ensure we update the convergence criteria + -- from SIESTA (in this way one can ensure siesta options) + for img = 1, NEB.n_images do + IOprint(("\nLUA NEB relaxation method for image %d:"):format(img)) + for i = 1, #relax[img] do + relax[img][i].tolerance = siesta.MD.MaxForceTol * Unit.Ang / Unit.eV + relax[img][i].max_dF = siesta.MD.MaxDispl / Unit.Ang + + -- Print information for this relaxation method + if siesta.IONode then + relax[img][i]:info() + end + end + end + + -- This is only reached one time, and that it as the beginning... + -- be sure to set the corresponding values + siesta.geom.xa = NEB.initial.R * Unit.Ang + + IOprint("\nLUA/NEB initial state\n") + -- force the initial image to be the first one to run + current_image = 0 + siesta_update_DM(0, current_image) + --Write xyz File + siesta_update_xyz(current_image) + IOprint(NEB[current_image].R) + + ret_tbl = {'geom.xa'} + + end + + if siesta.state == siesta.MOVE then + + -- Here we are doing the actual LBFGS algorithm. + -- We retrieve the current coordinates, the forces + -- and whether the geometry has relaxed + siesta.receive({"geom.fa", + "E.total", + "MD.Relaxed"}) + + -- Store the old image that has been tested, + -- in this way we can check whether we have moved to + -- a new image. + local old_image = current_image + + ret_tbl = siesta_move(siesta) + + -- we need to re-organize the DM files for faster convergence + -- pass whether the image is the same + siesta_update_DM(old_image, current_image) + siesta_update_xyz(current_image) + IOprint(NEB[current_image].R) + + end + + siesta.send(ret_tbl) +end + +function siesta_move(siesta) + + -- Retrieve the atomic coordinates, forces and the energy + local fa = flos.Array.from(siesta.geom.fa) * Unit.Ang / Unit.eV + local E = siesta.E.total / Unit.eV + + -- First update the coordinates, forces and energy for the + -- just calculated image + NEB[current_image]:set{F=fa, E=E} + + if current_image == 0 then + -- Perform the final image, to retain that information + current_image = NEB.n_images + 1 + + -- Set the atomic coordinates for the final image + siesta.geom.xa = NEB[current_image].R * Unit.Ang + + IOprint("\nLUA/NEB final state\n") + --siesta_update_DM(0, current_image) + -- The siesta relaxation is already not set + return {'geom.xa'} + + elseif current_image == NEB.n_images + 1 then + + -- Start the NEB calculation + current_image = 1 + + -- Set the atomic coordinates for the final image + siesta.geom.xa = NEB[current_image].R * Unit.Ang + + IOprint(("\nLUA/NEB running NEB image %d / %d\n"):format(current_image, NEB.n_images)) + + -- The siesta relaxation is already not set + return {'geom.xa'} + + elseif current_image < NEB.n_images then + + current_image = current_image + 1 + + -- Set the atomic coordinates for the image + siesta.geom.xa = NEB[current_image].R * Unit.Ang + + IOprint(("\nLUA/NEB running NEB image %d / %d\n"):format(current_image, NEB.n_images)) + + -- The siesta relaxation is already not set + return {'geom.xa'} + + end + + -- First we figure out how perform the NEB optimizations + -- Now we have calculated all the systems and are ready for doing + -- an NEB MD step + + -- Global variable to check for the NEB convergence + -- Initially assume it has relaxed + local relaxed = true + + IOprint("\nNEB step") + local out_R = {} + + -- loop on all images and pass the updated forces to the mixing algorithm + for img = 1, NEB.n_images do + + -- Get the correct NEB force (note that the relaxation + -- methods require the negative force) + local F = NEB:force(img, siesta.IONode) + IOprint("NEB: max F on image ".. img .. + (" = %10.5f, climbing = %s"):format(F:norm():max(), + tostring(NEB:climbing(img))) ) + + -- Prepare the relaxation for image `img` + local all_xa, weight = {}, flos.Array( #relax[img] ) + for i = 1, #relax[img] do + all_xa[i] = relax[img][i]:optimize(NEB[img].R, F) + weight[i] = relax[img][i].weight + end + weight = weight / weight:sum() + + if #relax[img] > 1 then + IOprint("\n weighted average for relaxation: ", tostring(weight)) + end + + -- Calculate the new coordinates and figure out + -- if the algorithm has converged (all forces below) + local out_xa = all_xa[1] * weight[1] + relaxed = relaxed and relax[img][1]:optimized() + for i = 2, #relax[img] do + out_xa = out_xa + all_xa[i] * weight[i] + relaxed = relaxed and relax[img][i]:optimized() + end + + -- Copy the optimized coordinates to a table + out_R[img] = out_xa + + end + + -- Before we update the coordinates we will write + -- the current steps results to the result file + -- (this HAS to be done before updating the coordinates) + NEB:save( siesta.IONode ) + + -- Now we may copy over the coordinates (otherwise + -- we do a consecutive update, and then overwrite) + for img = 1, NEB.n_images do + NEB[img]:set{R=out_R[img]} + end + + -- Start over in case the system has not relaxed + current_image = 1 + if relaxed then + -- the final coordinates are returned + siesta.geom.xa = NEB.final.R * Unit.Ang + IOprint("\nLUA/NEB complete\n") + else + siesta.geom.xa = NEB[1].R * Unit.Ang + IOprint(("\nLUA/NEB running NEB image %d / %d\n"):format(current_image, NEB.n_images)) + end + + siesta.MD.Relaxed = relaxed + + return {"geom.xa", + "MD.Relaxed"} +end + +-- Function for retaining the DM files for the images so that we +-- can easily restart etc. +function siesta_update_DM(old, current) + + if not siesta.IONode then + -- only allow the IOnode to perform stuff... + return + end + -- Move about files so that we re-use old DM files + local DM = label .. ".DM" + local old_DM = DM .. "." .. tostring(old) + local current_DM = DM .. "." .. tostring(current) + local initial_DM = DM .. ".0" + local final_DM = DM .. ".".. tostring(NEB.n_images+1) + print ("The Label of Old DM is : " .. old_DM) + print ("The Label of Current DM is : " .. current_DM) + -- Saving initial DM + if old==0 and current==0 then + print("Removing DM for Resuming") + IOprint("Deleting " .. DM .. " for a clean restart...") + os.execute("rm " .. DM) + end + + if 0 <= old and old <= NEB.n_images+1 and NEB:file_exists(DM) then + -- store the current DM for restart purposes + IOprint("Saving " .. DM .. " to " .. old_DM) + os.execute("mv " .. DM .. " " .. old_DM) + elseif NEB:file_exists(DM) then + IOprint("Deleting " .. DM .. " for a clean restart...") + os.execute("rm " .. DM) + end + + if NEB:file_exists(current_DM) then + IOprint("Deleting " .. DM .. " for a clean restart...") + os.execute("rm " .. DM) + IOprint("Restoring " .. current_DM .. " to " .. DM) + os.execute("cp " .. current_DM .. " " .. DM) + end + +end + +function siesta_update_xyz(current) + if not siesta.IONode then + -- only allow the IOnode to perform stuff... + return + end + local xyz_label = f_label_xyz ..tostring(current)..".xyz" + --self:_n_images=self.n_images + --self:_check_image(image) + + local f=io.open(xyz_label,"w") + f:write(tostring(#NEB[current].R).."\n \n") + --f:write(tostring(initialize:self.n_images).."\n \n") + for i=1,#NEB[current].R do + f:write(string.format(" %19.17f",tostring(NEB[current].R[i][1])).. " "..string.format("%19.17f",tostring(NEB[current].R[i][2]))..string.format(" %19.17f",tostring(NEB[current].R[i][3])).."\n") + end + f:close() + -- +end \ No newline at end of file diff --git a/examples/tneb_with_restart-new.lua b/examples/tneb_with_restart-new.lua new file mode 100644 index 0000000..3b0256a --- /dev/null +++ b/examples/tneb_with_restart-new.lua @@ -0,0 +1,344 @@ +--[[ +Example on how to use an NEB method. +--]] +--================================================================= +local image_label = "image_" +-- Total number of images (excluding initial[0] and final[n_images+1]) +local n_images = 5 +local k_spring = 1 +--================================================================= +-- Load the FLOS module +local flos = require "flos" +-- The prefix of the files that contain the images +-- Table of image geometries +local images = {} + +-- The default output label of the DM files +-- Function for reading a geometry +local read_geom = function(filename) + local file = io.open(filename, "r") + local na = tonumber(file:read()) + local R = flos.Array.zeros(na, 3) + file:read() + local i = 0 + local function tovector(s) + local t = {} + s:gsub('%S+', function(n) t[#t+1] = tonumber(n) end) + return t + end + for i = 1, na do + local line = file:read() + if line == nil then break end + -- Get stuff into the R + local v = tovector(line) + R[i][1] = v[1] + R[i][2] = v[2] + R[i][3] = v[3] + end + file:close() + return R +end + +-- Now read in the images +for i = 0, n_images + 1 do + images[#images+1] = flos.MDStep{R=read_geom(image_label .. i .. ".xyz")} +end + +-- Now we have all images... +local NEB = flos.TNEB(images,{k=k_spring,neb_temp=3000.}) +if siesta.IONode then + NEB:info() +end +-- Remove global (we use NEB.n_images) +n_images = nil + +-- Setup each image relaxation method (note it is prepared for several +-- relaxation methods per-image) +local relax = {} +for i = 1, NEB.n_images do + -- Select the relaxation method + relax[i] = {} + relax[i][1] = flos.CG{beta='PR',restart='Powell', line=flos.Line{optimizer = flos.LBFGS{H0 = 1. / 25.} } } + -- add more relaxation schemes if needed ;) + --relax[i][2] = flos.CG{beta='PR',restart='Powell', line=flos.Line{optimizer = flos.LBFGS{H0 = 1. / 50.} } } + --relax[i][3] = flos.CG{beta='PR',restart='Powell', line=flos.Line{optimizer = flos.LBFGS{H0 = 1. / 75.} } } + --relax[i][4] = flos.LBFGS{H0 = 1. / 50} + --relax[i][5] = flos.FIRE{dt_init = 1., direction="global", correct="global"} + if siesta.IONode then + NEB:info() + end + +end + +-- Counter for controlling which image we are currently relaxing +local current_image = 1 + +-- Grab the unit table of siesta (it is already created +-- by SIESTA) +local Unit = siesta.Units + + +function siesta_comm() + + -- This routine does exchange of data with SIESTA + local ret_tbl = {} + + -- Do the actual communication with SIESTA + if siesta.state == siesta.INITIALIZE then + + -- In the initialization step we request the + -- convergence criteria + -- MD.MaxDispl + -- MD.MaxForceTol + siesta.receive({"Label", + "geom.xa", + "MD.MaxDispl", + "MD.MaxForceTol"}) + + -- Store the Label + label = tostring(siesta.Label) + + -- Print information + IOprint("\nLUA NEB calculator") + + -- Ensure we update the convergence criteria + -- from SIESTA (in this way one can ensure siesta options) + for img = 1, NEB.n_images do + IOprint(("\nLUA NEB relaxation method for image %d:"):format(img)) + for i = 1, #relax[img] do + relax[img][i].tolerance = siesta.MD.MaxForceTol * Unit.Ang / Unit.eV + relax[img][i].max_dF = siesta.MD.MaxDispl / Unit.Ang + + -- Print information for this relaxation method + if siesta.IONode then + relax[img][i]:info() + end + end + end + + -- This is only reached one time, and that it as the beginning... + -- be sure to set the corresponding values + siesta.geom.xa = NEB.initial.R * Unit.Ang + + IOprint("\nLUA/NEB initial state\n") + -- force the initial image to be the first one to run + current_image = 0 + siesta_update_DM(0, current_image) + --Write xyz File + siesta_update_xyz(current_image) + IOprint(NEB[current_image].R) + + ret_tbl = {'geom.xa'} + + end + + if siesta.state == siesta.MOVE then + + -- Here we are doing the actual LBFGS algorithm. + -- We retrieve the current coordinates, the forces + -- and whether the geometry has relaxed + siesta.receive({"geom.fa", + "E.total", + "MD.Relaxed"}) + + -- Store the old image that has been tested, + -- in this way we can check whether we have moved to + -- a new image. + local old_image = current_image + + ret_tbl = siesta_move(siesta) + + -- we need to re-organize the DM files for faster convergence + -- pass whether the image is the same + siesta_update_DM(old_image, current_image) + siesta_update_xyz(current_image) + IOprint(NEB[current_image].R) + + end + + siesta.send(ret_tbl) +end + +function siesta_move(siesta) + + -- Retrieve the atomic coordinates, forces and the energy + local fa = flos.Array.from(siesta.geom.fa) * Unit.Ang / Unit.eV + local E = siesta.E.total / Unit.eV + + -- First update the coordinates, forces and energy for the + -- just calculated image + NEB[current_image]:set{F=fa, E=E} + + if current_image == 0 then + -- Perform the final image, to retain that information + current_image = NEB.n_images + 1 + + -- Set the atomic coordinates for the final image + siesta.geom.xa = NEB[current_image].R * Unit.Ang + + IOprint("\nLUA/NEB final state\n") + --siesta_update_DM(0, current_image) + -- The siesta relaxation is already not set + return {'geom.xa'} + + elseif current_image == NEB.n_images + 1 then + + -- Start the NEB calculation + current_image = 1 + + -- Set the atomic coordinates for the final image + siesta.geom.xa = NEB[current_image].R * Unit.Ang + + IOprint(("\nLUA/NEB running NEB image %d / %d\n"):format(current_image, NEB.n_images)) + + -- The siesta relaxation is already not set + return {'geom.xa'} + + elseif current_image < NEB.n_images then + + current_image = current_image + 1 + + -- Set the atomic coordinates for the image + siesta.geom.xa = NEB[current_image].R * Unit.Ang + + IOprint(("\nLUA/NEB running NEB image %d / %d\n"):format(current_image, NEB.n_images)) + + -- The siesta relaxation is already not set + return {'geom.xa'} + + end + + -- First we figure out how perform the NEB optimizations + -- Now we have calculated all the systems and are ready for doing + -- an NEB MD step + + -- Global variable to check for the NEB convergence + -- Initially assume it has relaxed + local relaxed = true + + IOprint("\nNEB step") + local out_R = {} + + -- loop on all images and pass the updated forces to the mixing algorithm + for img = 1, NEB.n_images do + + -- Get the correct NEB force (note that the relaxation + -- methods require the negative force) + local F = NEB:force(img, siesta.IONode) + IOprint("NEB: max F on image ".. img .. + (" = %10.5f, climbing = %s"):format(F:norm():max(), + tostring(NEB:climbing(img))) ) + + -- Prepare the relaxation for image `img` + local all_xa, weight = {}, flos.Array( #relax[img] ) + for i = 1, #relax[img] do + all_xa[i] = relax[img][i]:optimize(NEB[img].R, F) + weight[i] = relax[img][i].weight + end + weight = weight / weight:sum() + + if #relax[img] > 1 then + IOprint("\n weighted average for relaxation: ", tostring(weight)) + end + + -- Calculate the new coordinates and figure out + -- if the algorithm has converged (all forces below) + local out_xa = all_xa[1] * weight[1] + relaxed = relaxed and relax[img][1]:optimized() + for i = 2, #relax[img] do + out_xa = out_xa + all_xa[i] * weight[i] + relaxed = relaxed and relax[img][i]:optimized() + end + + -- Copy the optimized coordinates to a table + out_R[img] = out_xa + + end + + -- Before we update the coordinates we will write + -- the current steps results to the result file + -- (this HAS to be done before updating the coordinates) + NEB:save( siesta.IONode ) + + -- Now we may copy over the coordinates (otherwise + -- we do a consecutive update, and then overwrite) + for img = 1, NEB.n_images do + NEB[img]:set{R=out_R[img]} + end + + -- Start over in case the system has not relaxed + current_image = 1 + if relaxed then + -- the final coordinates are returned + siesta.geom.xa = NEB.final.R * Unit.Ang + IOprint("\nLUA/NEB complete\n") + else + siesta.geom.xa = NEB[1].R * Unit.Ang + IOprint(("\nLUA/NEB running NEB image %d / %d\n"):format(current_image, NEB.n_images)) + end + + siesta.MD.Relaxed = relaxed + + return {"geom.xa", + "MD.Relaxed"} +end + +-- Function for retaining the DM files for the images so that we +-- can easily restart etc. +function siesta_update_DM(old, current) + + if not siesta.IONode then + -- only allow the IOnode to perform stuff... + return + end + -- Move about files so that we re-use old DM files + local DM = label .. ".DM" + local old_DM = DM .. "." .. tostring(old) + local current_DM = DM .. "." .. tostring(current) + local initial_DM = DM .. ".0" + local final_DM = DM .. ".".. tostring(NEB.n_images+1) + print ("The Label of Old DM is : " .. old_DM) + print ("The Label of Current DM is : " .. current_DM) + -- Saving initial DM + if old==0 and current==0 then + print("Removing DM for Resuming") + IOprint("Deleting " .. DM .. " for a clean restart...") + os.execute("rm " .. DM) + end + + if 0 <= old and old <= NEB.n_images+1 and NEB:file_exists(DM) then + -- store the current DM for restart purposes + IOprint("Saving " .. DM .. " to " .. old_DM) + os.execute("mv " .. DM .. " " .. old_DM) + elseif NEB:file_exists(DM) then + IOprint("Deleting " .. DM .. " for a clean restart...") + os.execute("rm " .. DM) + end + + if NEB:file_exists(current_DM) then + IOprint("Deleting " .. DM .. " for a clean restart...") + os.execute("rm " .. DM) + IOprint("Restoring " .. current_DM .. " to " .. DM) + os.execute("cp " .. current_DM .. " " .. DM) + end + +end + +function siesta_update_xyz(current) + if not siesta.IONode then + -- only allow the IOnode to perform stuff... + return + end + local xyz_label = image_label ..tostring(current)..".xyz" + --self:_n_images=self.n_images + --self:_check_image(image) + + local f=io.open(xyz_label,"w") + f:write(tostring(#NEB[current].R).."\n \n") + --f:write(tostring(initialize:self.n_images).."\n \n") + for i=1,#NEB[current].R do + f:write(string.format(" %19.17f",tostring(NEB[current].R[i][1])).. " "..string.format("%19.17f",tostring(NEB[current].R[i][2]))..string.format(" %19.17f",tostring(NEB[current].R[i][3])).."\n") + end + f:close() + -- +end diff --git a/examples/vc-dneb_with_restart.lua b/examples/vc-dneb_with_restart.lua new file mode 100644 index 0000000..9903bc9 --- /dev/null +++ b/examples/vc-dneb_with_restart.lua @@ -0,0 +1,484 @@ +--[[ +Example on how to use an NEB method. +--]] +-- Load the FLOS module +local flos = require "flos" +-- The prefix of the files that contain the images +local image_label = "image_coordinates_" +local image_vector_label= "image_vectors_" +-- Total number of images (excluding initial[0] and final[n_images+1]) +local n_images = 5 +-- Table of image geometries +local images = {} +local images_vectors={} +-- The default output label of the DM files +--local label = "MgO-3x3x1-2V" +local f_label_xyz = image_label --"image_coordinates_" +local f_label_xyz_vec = image_vector_label --"image_vectors_" +-- Function for reading a geometry of vector +local read_geom_vec = function(filename) + local file = io.open(filename, "r") + local na = tonumber(file:read()) + local R = flos.Array.zeros(na, 3) + file:read() + local i = 0 + local function tovector(s) + local t = {} + s:gsub('%S+', function(n) t[#t+1] = tonumber(n) end) + return t + end + for i = 1, na do + local line = file:read() + if line == nil then break end + -- Get stuff into the R + local v = tovector(line) + R[i][1] = v[1] + R[i][2] = v[2] + R[i][3] = v[3] + end + file:close() + return R +end +-- Function for reading a geometry +local read_geom = function(filename) + local file = io.open(filename, "r") + local na = tonumber(file:read()) + local R = flos.Array.zeros(na, 3) + file:read() + local i = 0 + local function tovector(s) + local t = {} + s:gsub('%S+', function(n) t[#t+1] = tonumber(n) end) + return t + end + for i = 1, na do + local line = file:read() + if line == nil then break end + -- Get stuff into the R + local v = tovector(line) + R[i][1] = v[1] + R[i][2] = v[2] + R[i][3] = v[3] + end + file:close() + return R +end +-- Now read in the images +for i = 0, n_images + 1 do + images[#images+1] = flos.MDStep{R=read_geom(image_label .. i .. ".xyz")} + images_vectors[#images_vectors+1]= flos.MDStep{R=read_geom_vec(image_vector_label .. i .. ".xyz")} +end +-- Now we have all images... +local NEB = flos.VCDNEB(images,{k=0.01}) +local VCNEB = flos.VCDNEB(images_vectors,{k=0.01}) +--NEB.DM_label=labe --"MgO-3x3x1-2V" +if siesta.IONode then + NEB:info() + VCNEB:info() +end +-- Remove global (we use NEB.n_images) +n_images = nil +-- Setup each image relaxation method (note it is prepared for several +-- relaxation methods per-image) +local relax = {} +local vcrelax= {} +for i=1, NEB.n_images do + relax[i]={} + vcrelax[i]={} + relax[i][1] = flos.CG{beta='PR', line=flos.Line{optimizer = flos.LBFGS{H0 = 1. / 25.} } } + vcrelax[i][1] = flos.CG{beta='PR', line=flos.Line{optimizer = flos.LBFGS{H0 = 1. / 75.} } } + if siesta.IONode then + NEB:info() + VCNEB:info() + end + --relax[i][2] = flos.LBFGS{H0 = 1. / 50} + --relax[i][1] = flos.FIRE{dt_init = 1., direction="global", correct="global"} + -- add more relaxation schemes if needed ;) +end +-- Counter for controlling which image we are currently relaxing +local current_image = 1 +-- Grab the unit table of siesta (it is already created +-- by SIESTA) +local Unit = siesta.Units +function siesta_comm() + -- This routine does exchange of data with SIESTA + local ret_tbl = {} + -- Do the actual communication with SIESTA + if siesta.state == siesta.INITIALIZE then + -- In the initialization step we request the + -- convergence criteria + -- MD.MaxDispl + -- MD.MaxForceTol + siesta.receive({"Label", + "geom.xa", + "MD.MaxDispl", + "MD.MaxForceTol", + "MD.MaxStressTol", + "geom.cell", + "geom.stress"}) + -- Store the Label + label = tostring(siesta.Label) + --stress=flos.Array.from(siesta.geom.stress)* Unit.Ang ^ 3 / Unit.eV + -- Print information + IOprint("\nLUA NEB calculator") + -- Ensure we update the convergence criteria + -- from SIESTA (in this way one can ensure siesta options) + for img = 1, NEB.n_images do + IOprint(("\nLUA NEB relaxation method for image %d:"):format(img)) + for i = 1, #relax[img] do + relax[img][i].tolerance = siesta.MD.MaxForceTol * Unit.Ang / Unit.eV + relax[img][i].max_dF = siesta.MD.MaxDispl / Unit.Ang + vcrelax[img][i].tolerance = siesta.MD.MaxStressTol * Unit.Ang ^ 3 / Unit.eV + vcrelax[img][i].max_dF = siesta.MD.MaxDispl / Unit.Ang + -- Print information for this relaxation method + if siesta.IONode then + relax[img][i]:info() + vcrelax[img][i]:info() + end + end + end + -- This is only reached one time, and that it as the beginning... + -- be sure to set the corresponding values + siesta.geom.xa = NEB.initial.R * Unit.Ang + siesta.geom.cell = VCNEB.initial.R * Unit.Ang + IOprint("\nLUA/NEB initial state\n") + -- force the initial image to be the first one to run + --IOprint(VCNEB.zeros) + current_image = 0 + siesta_update_DM(0, current_image) + --Write xyz File + siesta_update_xyz(current_image) + siesta_update_xyz_vec(current_image) + IOprint("============================================") + IOprint("Lattice Vector") + IOprint(VCNEB[current_image].R) + IOprint("============================================") + IOprint("Atomic Coordinates") + IOprint(NEB[current_image].R) + IOprint("============================================") + ret_tbl = {'geom.xa',"geom.stress","geom.cell"} + end + if siesta.state == siesta.MOVE then + -- Here we are doing the actual LBFGS algorithm. + -- We retrieve the current coordinates, the forces + -- and whether the geometry has relaxed + siesta.receive({"geom.fa", + "E.total", + "MD.Relaxed", + "geom.cell", + "geom.stress"}) + -- Store the old image that has been tested, + -- in this way we can check whether we have moved to + -- a new image. + local old_image = current_image + ret_tbl = siesta_move(siesta) + -- we need to re-organize the DM files for faster convergence + -- pass whether the image is the same + --stress=flos.Array.from(siesta.geom.stress)* Unit.Ang ^ 3 / Unit.eV + siesta_update_DM(old_image, current_image) + siesta_update_xyz(current_image) + siesta_update_xyz_vec(current_image) + --IOprint(stress) + end + siesta.send(ret_tbl) +end +function siesta_move(siesta) + -- Retrieve the atomic coordinates, forces and the energy + local fa = flos.Array.from(siesta.geom.fa) * Unit.Ang / Unit.eV + local E = siesta.E.total / Unit.eV + -- First update the coordinates, forces and energy for the + -- just calculated image + --print(fa) + NEB[current_image]:set{F=fa, E=E} + --[[ Retrieve the vector coordinates, forces and the energy --]] + --local cell=flos.Array.from(siesta.geom.cell)/ Unit.Ang + --local vol=cell[1]:cross(cell[2]):dot(cell[3]) + local Vfa = (-flos.Array.from(siesta.geom.stress) * Unit.Ang ^ 3 / Unit.eV)--* vol + local VE = siesta.E.total / Unit.eV + -- First update the coordinates, forces and energy for the + -- just calculated image + --print(Vfa) + VCNEB[current_image]:set{F=Vfa,E=VE} + --VCNEB:force(current_image, siesta.IONode) + if current_image == 0 then + -- Perform the final image, to retain that information + current_image = NEB.n_images + 1 + -- Set the atomic coordinates for the final image + siesta.geom.xa = NEB[current_image].R * Unit.Ang + siesta.geom.cell = VCNEB[current_image].R * Unit.Ang + IOprint("\nLUA/NEB final state\n") + IOprint("Lattice Vectors") + IOprint(VCNEB[current_image].R) + IOprint("Stresss") + IOprint(VCNEB[current_image].F) + --IOprint(stress) + -- The siesta relaxation is already not set + return {'geom.xa',"geom.stress","geom.cell"} + elseif current_image == NEB.n_images + 1 then + -- Start the NEB calculation + current_image = 1 + -- Set the atomic coordinates for the final image + siesta.geom.xa = NEB[current_image].R * Unit.Ang + siesta.geom.cell = VCNEB[current_image].R * Unit.Ang + IOprint(("\nLUA/NEB running NEB image %d / %d\n"):format(current_image, NEB.n_images)) + IOprint("Lattice Vectors") + IOprint(VCNEB[current_image].R) + IOprint("Stresss") + IOprint(VCNEB[current_image].F) + -- The siesta relaxation is already not set + return {'geom.xa',"geom.stress","geom.cell"} + elseif current_image < NEB.n_images then + current_image = current_image + 1 + -- Set the atomic coordinates for the image + siesta.geom.xa = NEB[current_image].R * Unit.Ang + siesta.geom.cell = VCNEB[current_image].R * Unit.Ang + IOprint(("\nLUA/NEB running NEB image %d / %d\n"):format(current_image, NEB.n_images)) + IOprint("Lattice Vectors") + IOprint(VCNEB[current_image].R) + IOprint("Stresss") + IOprint(VCNEB[current_image].F) + --IOprint(NEB.tangent) + -- The siesta relaxation is already not set + return {'geom.xa',"geom.stress","geom.cell"} + end + -- First we figure out how perform the NEB optimizations + -- Now we have calculated all the systems and are ready for doing + -- an NEB MD step + -- Global variable to check for the NEB convergence + -- Initially assume it has relaxed + local relaxed = true + local vcrelaxed = true + local tot_relax= false + IOprint("\nNEB step") + local out_R = {} + local out_VR = {} + -- loop on all images and pass the updated forces to the mixing algorithm + for img = 1, NEB.n_images do + -- Get the correct NEB force (note that the relaxation + -- methods require the negative force) + local F = NEB:force(img, siesta.IONode) + IOprint("NEB: max F on image ".. img .. + (" = %10.5f, climbing = %s"):format(F:norm():max(), + tostring(NEB:climbing(img))) ) + -- Prepare the relaxation for image `img` + local all_xa, weight = {}, flos.Array( #relax[img] ) + for i = 1, #relax[img] do + all_xa[i] = relax[img][i]:optimize(NEB[img].R, F) + weight[i] = relax[img][i].weight + end + weight = weight / weight:sum() + if #relax[img] > 1 then + IOprint("\n weighted average for relaxation: ", tostring(weight)) + end + -- Calculate the new coordinates and figure out + -- if the algorithm has converged (all forces below) + local out_xa = all_xa[1] * weight[1] + relaxed = relaxed and relax[img][1]:optimized() + for i = 2, #relax[img] do + out_xa = out_xa + all_xa[i] * weight[i] + relaxed = relaxed and relax[img][i]:optimized() + end + -- Copy the optimized coordinates to a table + --out_R[img] = out_xa + --================================================================- + -- For Lattice Optimization + --================================================================- + local icell = VCNEB[img].R --/ Unit.Ang + --local all_strain={} + local ivol=icell[1]:cross(icell[2]):dot(icell[3]) + local strain=flos.Array.zeros(6) + local stress_mask=flos.Array.ones(6) + stress_mask[3]=0.0 + stress_mask[4]=0.0 + stress_mask[5]=0.0 + stress_mask[6]=0.0 + local stress=-stress_to_voigt(siesta.geom.stress)--* Unit.Ang ^ 3 / Unit.eV + stress = stress * stress_mask + local VF = VCNEB:force(img, siesta.IONode) + IOprint("VCNEB: max Strain F on image ".. img .. + (" = %10.5f, climbing = %s"):format(VF:norm():max(), + tostring(VCNEB:climbing(img))) ) + IOprint(VCNEB[img].F) + local all_vcxa, vcweight = {}, flos.Array( #vcrelax[img] ) + for i = 1, #vcrelax[img] do + all_vcxa[i] = vcrelax[img][i]:optimize(strain, stress )--* ivol + vcweight[i] = vcrelax[img][i].weight + end + vcweight = vcweight / vcweight:sum() + if #vcrelax[img] > 1 then + IOprint("\n weighted average for cell relaxation: ", tostring(vcweight)) + end + -- Calculate the new coordinates and figure out + -- if the algorithm has converged (all forces below) + local out_vcxa = all_vcxa[1] * vcweight[1] + vcrelaxed = vcrelaxed and vcrelax[img][1]:optimized() + for i = 2, #relax[img] do + out_vcxa = out_vcxa + all_vcxa[i] * vcweight[i] + vcrelaxed = vcrelaxed and vcrelax[img][i]:optimized() + end + + --local out_strain=all_strain[1]*vcweight[1] + all_vcxa = nil --all_strain = nil + strain = out_vcxa * stress_mask --strain = out_strain * stress_mask + out_vcxa = nil --strain = out_strain * stress_mask --out_strain = nil + local dcell = flos.Array(icell.shape) + dcell[1][1]=1.0 + strain[1] + dcell[1][2]=0.5 * strain[6] + dcell[1][3]=0.5 * strain[5] + dcell[2][1]=0.5 * strain[6] + dcell[2][2]=1.0 + strain[2] + --dcell[2][2]=1.0 + strain[1] + dcell[2][3]=0.5 * strain[4] + dcell[3][1]=0.5 * strain[5] + dcell[3][2]=0.5 * strain[4] + dcell[3][3]=1.0 + strain[3] + local out_cell=icell:dot(dcell) + --local out_cell=icell+dcell + --print ("stress") + --print(stress) + --print("cell out") + --print (out_cell) + dcell = nil + local lat = flos.Lattice:new(icell) + local fxa = lat:fractional(out_xa) + xa =fxa:dot(out_cell) + lat = nil + fxa = nil + -- Copy the optimized vectors to a table + out_VR[img] = out_cell + -- Copy the optimized coordinates with respecto to new optimized vectors to a table + out_R[img] = xa + --================================================================-- + end + + -- Before we update the coordinates we will write + -- the current steps results to the result file + -- (this HAS to be done before updating the coordinates) + NEB:save( siesta.IONode ) + + -- Now we may copy over the coordinates (otherwise + -- we do a consecutive update, and then overwrite) + for img = 1, NEB.n_images do + NEB[img]:set{R=out_R[img]} + VCNEB[img]:set{R=out_VR[img]} + end + -- Start over in case the system has not relaxed + current_image = 1 + if relaxed and vcrelaxed then + tot_relax= true + -- the final coordinates are returned + siesta.geom.xa = NEB.final.R * Unit.Ang + siesta.geom.cell = VCNEB.final.R * Unit.Ang + IOprint("\nLUA/NEB complete\n") + else + siesta.geom.xa = NEB[1].R * Unit.Ang + siesta.geom.cell = VCNEB[1].R * Unit.Ang + IOprint(("\nLUA/NEB running NEB image %d / %d\n"):format(current_image, NEB.n_images)) + IOprint("Lattice Vectors") + IOprint(VCNEB[1].R) + IOprint("Stresss") + IOprint(VCNEB[1].F) + end + siesta.MD.Relaxed = tot_relax + return {"geom.xa","geom.stress","geom.cell", + "MD.Relaxed"} +end +--[[ +function file_exists(name) + local f = io.open(name, "r") + if f ~= nil then + io.close(f) + return true + else + return false + end +end--]] + +-- Function for retaining the DM files for the images so that we +-- can easily restart etc. +function siesta_update_DM(old, current) + + if not siesta.IONode then + -- only allow the IOnode to perform stuff... + return + end + -- Move about files so that we re-use old DM files + local DM = label .. ".DM" + local old_DM = DM .. "." .. tostring(old) + local current_DM = DM .. "." .. tostring(current) + local initial_DM = DM .. ".0" + local final_DM = DM .. ".".. tostring(NEB.n_images+1) + print ("The Label of Old DM is : " .. old_DM) + print ("The Label of Current DM is : " .. current_DM) + -- Saving initial DM + if old==0 and current==0 then + print("Removing DM for Resuming") + IOprint("Deleting " .. DM .. " for a clean restart...") + os.execute("rm " .. DM) + end + + if 0 <= old and old <= NEB.n_images+1 and NEB:file_exists(DM) then + -- store the current DM for restart purposes + IOprint("Saving " .. DM .. " to " .. old_DM) + os.execute("mv " .. DM .. " " .. old_DM) + elseif NEB:file_exists(DM) then + IOprint("Deleting " .. DM .. " for a clean restart...") + os.execute("rm " .. DM) + end + + if NEB:file_exists(current_DM) then + IOprint("Deleting " .. DM .. " for a clean restart...") + os.execute("rm " .. DM) + IOprint("Restoring " .. current_DM .. " to " .. DM) + os.execute("cp " .. current_DM .. " " .. DM) + end + +end + +function stress_to_voigt(stress) + local voigt = flos.Array.empty(6) + voigt[1]=stress[1][1] + voigt[2]=stress[2][2] + voigt[3]=stress[3][3] + voigt[4]=(stress[2][3]+stress[3][2])*0.5 + voigt[5]=(stress[1][3]+stress[3][1])*0.5 + voigt[6]=(stress[1][2]+stress[2][1])*0.5 + return voigt +end +function siesta_update_xyz(current) + if not siesta.IONode then + -- only allow the IOnode to perform stuff... + return + end + local xyz_label = f_label_xyz ..tostring(current)..".xyz" + --self:_n_images=self.n_images + --self:_check_image(image) + + local f=io.open(xyz_label,"w") + f:write(tostring(#NEB[current].R).."\n \n") + --f:write(tostring(initialize:self.n_images).."\n \n") + for i=1,#NEB[current].R do + f:write(string.format(" %19.17f",tostring(NEB[current].R[i][1])).. " "..string.format("%19.17f",tostring(NEB[current].R[i][2]))..string.format(" %19.17f",tostring(NEB[current].R[i][3])).."\n") + end + f:close() + -- +end + +function siesta_update_xyz_vec(current) + if not siesta.IONode then + -- only allow the IOnode to perform stuff... + return + end + local xyz_vec_label = f_label_xyz_vec ..tostring(current)..".xyz" + --self:_n_images=self.n_images + --self:_check_image(image) + + local f=io.open(xyz_vec_label,"w") + f:write(tostring(#VCNEB[current].R).."\n \n") + --f:write(tostring(initialize:self.n_images).."\n \n") + for i=1,#VCNEB[current].R do + f:write(string.format(" %19.17f",tostring(VCNEB[current].R[i][1])).. " "..string.format("%19.17f",tostring(VCNEB[current].R[i][2]))..string.format(" %19.17f",tostring(VCNEB[current].R[i][3])).."\n") + end + f:close() + -- +end diff --git a/examples/vc-neb_with_restart.lua b/examples/vc-neb_with_restart.lua new file mode 100644 index 0000000..1ffbd15 --- /dev/null +++ b/examples/vc-neb_with_restart.lua @@ -0,0 +1,486 @@ +--[[ +Example on how to use an NEB method. +--]] +-- Load the FLOS module +local flos = require "flos" +-- The prefix of the files that contain the images +local image_label = "image_coordinates_" +local image_vector_label= "image_vectors_" +-- Total number of images (excluding initial[0] and final[n_images+1]) +local n_images = 5 +-- Table of image geometries +local images = {} +local images_vectors={} +-- The default output label of the DM files +local label = "MgO-3x3x1-2V" +local f_label_xyz = "image_coordinates_" +local f_label_xyz_vec = "image_vectors_" +-- Function for reading a geometry of vector +local read_geom_vec = function(filename) + local file = io.open(filename, "r") + local na = tonumber(file:read()) + local R = flos.Array.zeros(na, 3) + file:read() + local i = 0 + local function tovector(s) + local t = {} + s:gsub('%S+', function(n) t[#t+1] = tonumber(n) end) + return t + end + for i = 1, na do + local line = file:read() + if line == nil then break end + -- Get stuff into the R + local v = tovector(line) + R[i][1] = v[1] + R[i][2] = v[2] + R[i][3] = v[3] + end + file:close() + return R +end +-- Function for reading a geometry +local read_geom = function(filename) + local file = io.open(filename, "r") + local na = tonumber(file:read()) + local R = flos.Array.zeros(na, 3) + file:read() + local i = 0 + local function tovector(s) + local t = {} + s:gsub('%S+', function(n) t[#t+1] = tonumber(n) end) + return t + end + for i = 1, na do + local line = file:read() + if line == nil then break end + -- Get stuff into the R + local v = tovector(line) + R[i][1] = v[1] + R[i][2] = v[2] + R[i][3] = v[3] + end + file:close() + return R +end +-- Now read in the images +for i = 0, n_images + 1 do + images[#images+1] = flos.MDStep{R=read_geom(image_label .. i .. ".xyz")} + images_vectors[#images_vectors+1]= flos.MDStep{R=read_geom_vec(image_vector_label .. i .. ".xyz")} +end +-- Now we have all images... +local NEB = flos.VCNEB(images) +local VCNEB = flos.VCNEB(images_vectors) +NEB.DM_label=labe --"MgO-3x3x1-2V" +if siesta.IONode then + NEB:info() + VCNEB:info() +end +-- Remove global (we use NEB.n_images) +n_images = nil +-- Setup each image relaxation method (note it is prepared for several +-- relaxation methods per-image) +local relax = {} +local vcrelax= {} +for i=1, NEB.n_images do + relax[i]={} + vcrelax[i]={} + relax[i][1] = flos.CG{beta='PR', line=flos.Line{optimizer = flos.LBFGS{H0 = 1. / 25.} } } + vcrelax[i][1] = flos.CG{beta='PR', line=flos.Line{optimizer = flos.LBFGS{H0 = 1. / 75.} } } + if siesta.IONode then + NEB:info() + VCNEB:info() + end + --relax[i][2] = flos.LBFGS{H0 = 1. / 50} + --relax[i][1] = flos.FIRE{dt_init = 1., direction="global", correct="global"} + -- add more relaxation schemes if needed ;) +end +-- Counter for controlling which image we are currently relaxing +local current_image = 1 +-- Grab the unit table of siesta (it is already created +-- by SIESTA) +local Unit = siesta.Units + +function siesta_comm() + -- This routine does exchange of data with SIESTA + local ret_tbl = {} + -- Do the actual communication with SIESTA + if siesta.state == siesta.INITIALIZE then + -- In the initialization step we request the + -- convergence criteria + -- MD.MaxDispl + -- MD.MaxForceTol + siesta.receive({"Label", + "geom.xa", + "MD.MaxDispl", + "MD.MaxForceTol", + "MD.MaxStressTol", + "geom.cell", + "geom.stress"}) + -- Store the Label + label = tostring(siesta.Label) + --stress=flos.Array.from(siesta.geom.stress)* Unit.Ang ^ 3 / Unit.eV + -- Print information + IOprint("\nLUA NEB calculator") + -- Ensure we update the convergence criteria + -- from SIESTA (in this way one can ensure siesta options) + for img = 1, NEB.n_images do + IOprint(("\nLUA NEB relaxation method for image %d:"):format(img)) + for i = 1, #relax[img] do + relax[img][i].tolerance = siesta.MD.MaxForceTol * Unit.Ang / Unit.eV + relax[img][i].max_dF = siesta.MD.MaxDispl / Unit.Ang + vcrelax[img][i].tolerance = siesta.MD.MaxStressTol * Unit.Ang ^ 3 / Unit.eV + vcrelax[img][i].max_dF = siesta.MD.MaxDispl / Unit.Ang + -- Print information for this relaxation method + if siesta.IONode then + relax[img][i]:info() + vcrelax[img][i]:info() + end + end + end + -- This is only reached one time, and that it as the beginning... + -- be sure to set the corresponding values + siesta.geom.xa = NEB.initial.R * Unit.Ang + siesta.geom.cell = VCNEB.initial.R * Unit.Ang + IOprint("\nLUA/NEB initial state\n") + -- force the initial image to be the first one to run + --IOprint(VCNEB.zeros) + current_image = 0 + siesta_update_DM(0, current_image) + --Write xyz File + siesta_update_xyz(current_image) + siesta_update_xyz_vec(current_image) + IOprint("============================================") + IOprint("Lattice Vector") + IOprint(VCNEB[current_image].R) + IOprint("============================================") + IOprint("Atomic Coordinates") + IOprint(NEB[current_image].R) + IOprint("============================================") + ret_tbl = {'geom.xa',"geom.stress","geom.cell"} + end + if siesta.state == siesta.MOVE then + -- Here we are doing the actual LBFGS algorithm. + -- We retrieve the current coordinates, the forces + -- and whether the geometry has relaxed + siesta.receive({"geom.fa", + "E.total", + "MD.Relaxed", + "geom.cell", + "geom.stress"}) + -- Store the old image that has been tested, + -- in this way we can check whether we have moved to + -- a new image. + local old_image = current_image + ret_tbl = siesta_move(siesta) + -- we need to re-organize the DM files for faster convergence + -- pass whether the image is the same + --stress=flos.Array.from(siesta.geom.stress)* Unit.Ang ^ 3 / Unit.eV + siesta_update_DM(old_image, current_image) + siesta_update_xyz(current_image) + siesta_update_xyz_vec(current_image) + --IOprint(stress) + end + siesta.send(ret_tbl) +end + +function siesta_move(siesta) + -- Retrieve the atomic coordinates, forces and the energy + local fa = flos.Array.from(siesta.geom.fa) * Unit.Ang / Unit.eV + local E = siesta.E.total / Unit.eV + -- First update the coordinates, forces and energy for the + -- just calculated image + --print(fa) + NEB[current_image]:set{F=fa, E=E} + --[[ Retrieve the vector coordinates, forces and the energy --]] + --local cell=flos.Array.from(siesta.geom.cell)/ Unit.Ang + --local vol=cell[1]:cross(cell[2]):dot(cell[3]) + local Vfa = (-flos.Array.from(siesta.geom.stress) * Unit.Ang ^ 3 / Unit.eV)--* vol + local VE = siesta.E.total / Unit.eV + -- First update the coordinates, forces and energy for the + -- just calculated image + --print(Vfa) + VCNEB[current_image]:set{F=Vfa,E=VE} + --VCNEB:force(current_image, siesta.IONode) + if current_image == 0 then + -- Perform the final image, to retain that information + current_image = NEB.n_images + 1 + -- Set the atomic coordinates for the final image + siesta.geom.xa = NEB[current_image].R * Unit.Ang + siesta.geom.cell = VCNEB[current_image].R * Unit.Ang + IOprint("\nLUA/NEB final state\n") + IOprint("Lattice Vectors") + IOprint(VCNEB[current_image].R) + IOprint("Stresss") + IOprint(VCNEB[current_image].F) + --IOprint(stress) + -- The siesta relaxation is already not set + return {'geom.xa',"geom.stress","geom.cell"} + elseif current_image == NEB.n_images + 1 then + -- Start the NEB calculation + current_image = 1 + -- Set the atomic coordinates for the final image + siesta.geom.xa = NEB[current_image].R * Unit.Ang + siesta.geom.cell = VCNEB[current_image].R * Unit.Ang + IOprint(("\nLUA/NEB running NEB image %d / %d\n"):format(current_image, NEB.n_images)) + IOprint("Lattice Vectors") + IOprint(VCNEB[current_image].R) + IOprint("Stresss") + IOprint(VCNEB[current_image].F) + -- The siesta relaxation is already not set + return {'geom.xa',"geom.stress","geom.cell"} + elseif current_image < NEB.n_images then + current_image = current_image + 1 + -- Set the atomic coordinates for the image + siesta.geom.xa = NEB[current_image].R * Unit.Ang + siesta.geom.cell = VCNEB[current_image].R * Unit.Ang + IOprint(("\nLUA/NEB running NEB image %d / %d\n"):format(current_image, NEB.n_images)) + IOprint("Lattice Vectors") + IOprint(VCNEB[current_image].R) + IOprint("Stresss") + IOprint(VCNEB[current_image].F) + --IOprint(NEB.tangent) + -- The siesta relaxation is already not set + return {'geom.xa',"geom.stress","geom.cell"} + end + -- First we figure out how perform the NEB optimizations + -- Now we have calculated all the systems and are ready for doing + -- an NEB MD step + -- Global variable to check for the NEB convergence + -- Initially assume it has relaxed + local relaxed = true + local vcrelaxed = true + local tot_relax= false + IOprint("\nNEB step") + local out_R = {} + local out_VR = {} + -- loop on all images and pass the updated forces to the mixing algorithm + for img = 1, NEB.n_images do + -- Get the correct NEB force (note that the relaxation + -- methods require the negative force) + local F = NEB:force(img, siesta.IONode) + IOprint("NEB: max F on image ".. img .. + (" = %10.5f, climbing = %s"):format(F:norm():max(), + tostring(NEB:climbing(img))) ) + -- Prepare the relaxation for image `img` + local all_xa, weight = {}, flos.Array( #relax[img] ) + for i = 1, #relax[img] do + all_xa[i] = relax[img][i]:optimize(NEB[img].R, F) + weight[i] = relax[img][i].weight + end + weight = weight / weight:sum() + if #relax[img] > 1 then + IOprint("\n weighted average for relaxation: ", tostring(weight)) + end + -- Calculate the new coordinates and figure out + -- if the algorithm has converged (all forces below) + local out_xa = all_xa[1] * weight[1] + relaxed = relaxed and relax[img][1]:optimized() + for i = 2, #relax[img] do + out_xa = out_xa + all_xa[i] * weight[i] + relaxed = relaxed and relax[img][i]:optimized() + end + -- Copy the optimized coordinates to a table + --out_R[img] = out_xa + --================================================================- + -- For Lattice Optimization + --================================================================- + local icell = VCNEB[img].R --/ Unit.Ang + --local all_strain={} + local ivol=icell[1]:cross(icell[2]):dot(icell[3]) + local strain=flos.Array.zeros(6) + local stress_mask=flos.Array.ones(6) + stress_mask[3]=0.0 + stress_mask[4]=0.0 + stress_mask[5]=0.0 + stress_mask[6]=0.0 + local stress=-stress_to_voigt(siesta.geom.stress)--* Unit.Ang ^ 3 / Unit.eV + stress = stress * stress_mask + local VF = VCNEB:force(img, siesta.IONode) + IOprint("VCNEB: max Strain F on image ".. img .. + (" = %10.5f, climbing = %s"):format(VF:norm():max(), + tostring(VCNEB:climbing(img))) ) + IOprint(VCNEB[img].F) + local all_vcxa, vcweight = {}, flos.Array( #vcrelax[img] ) + for i = 1, #vcrelax[img] do + all_vcxa[i] = vcrelax[img][i]:optimize(strain, stress )--* ivol + vcweight[i] = vcrelax[img][i].weight + end + vcweight = vcweight / vcweight:sum() + if #vcrelax[img] > 1 then + IOprint("\n weighted average for cell relaxation: ", tostring(vcweight)) + end + -- Calculate the new coordinates and figure out + -- if the algorithm has converged (all forces below) + local out_vcxa = all_vcxa[1] * vcweight[1] + vcrelaxed = vcrelaxed and vcrelax[img][1]:optimized() + for i = 2, #relax[img] do + out_vcxa = out_vcxa + all_vcxa[i] * vcweight[i] + vcrelaxed = vcrelaxed and vcrelax[img][i]:optimized() + end + + --local out_strain=all_strain[1]*vcweight[1] + all_vcxa = nil --all_strain = nil + strain = out_vcxa * stress_mask --strain = out_strain * stress_mask + out_vcxa = nil --strain = out_strain * stress_mask --out_strain = nil + local dcell = flos.Array(icell.shape) + dcell[1][1]=1.0 + strain[1] + dcell[1][2]=0.5 * strain[6] + dcell[1][3]=0.5 * strain[5] + dcell[2][1]=0.5 * strain[6] + dcell[2][2]=1.0 + strain[2] + --dcell[2][2]=1.0 + strain[1] + dcell[2][3]=0.5 * strain[4] + dcell[3][1]=0.5 * strain[5] + dcell[3][2]=0.5 * strain[4] + dcell[3][3]=1.0 + strain[3] + local out_cell=icell:dot(dcell) + --local out_cell=icell+dcell + --print ("stress") + --print(stress) + --print("cell out") + --print (out_cell) + dcell = nil + local lat = flos.Lattice:new(icell) + local fxa = lat:fractional(out_xa) + xa =fxa:dot(out_cell) + lat = nil + fxa = nil + -- Copy the optimized vectors to a table + out_VR[img] = out_cell + -- Copy the optimized coordinates with respecto to new optimized vectors to a table + out_R[img] = xa + --================================================================-- + end + + -- Before we update the coordinates we will write + -- the current steps results to the result file + -- (this HAS to be done before updating the coordinates) + NEB:save( siesta.IONode ) + + -- Now we may copy over the coordinates (otherwise + -- we do a consecutive update, and then overwrite) + for img = 1, NEB.n_images do + NEB[img]:set{R=out_R[img]} + VCNEB[img]:set{R=out_VR[img]} + end + -- Start over in case the system has not relaxed + current_image = 1 + if relaxed and vcrelaxed then + tot_relax= true + -- the final coordinates are returned + siesta.geom.xa = NEB.final.R * Unit.Ang + siesta.geom.cell = VCNEB.final.R * Unit.Ang + IOprint("\nLUA/NEB complete\n") + else + siesta.geom.xa = NEB[1].R * Unit.Ang + siesta.geom.cell = VCNEB[1].R * Unit.Ang + IOprint(("\nLUA/NEB running NEB image %d / %d\n"):format(current_image, NEB.n_images)) + IOprint("Lattice Vectors") + IOprint(VCNEB[1].R) + IOprint("Stresss") + IOprint(VCNEB[1].F) + end + siesta.MD.Relaxed = tot_relax + return {"geom.xa","geom.stress","geom.cell", + "MD.Relaxed"} +end +--[[ +function file_exists(name) + local f = io.open(name, "r") + if f ~= nil then + io.close(f) + return true + else + return false + end +end--]] + +-- Function for retaining the DM files for the images so that we +-- can easily restart etc. +function siesta_update_DM(old, current) + + if not siesta.IONode then + -- only allow the IOnode to perform stuff... + return + end + -- Move about files so that we re-use old DM files + local DM = label .. ".DM" + local old_DM = DM .. "." .. tostring(old) + local current_DM = DM .. "." .. tostring(current) + local initial_DM = DM .. ".0" + local final_DM = DM .. ".".. tostring(NEB.n_images+1) + print ("The Label of Old DM is : " .. old_DM) + print ("The Label of Current DM is : " .. current_DM) + -- Saving initial DM + if old==0 and current==0 then + print("Removing DM for Resuming") + IOprint("Deleting " .. DM .. " for a clean restart...") + os.execute("rm " .. DM) + end + + if 0 <= old and old <= NEB.n_images+1 and NEB:file_exists(DM) then + -- store the current DM for restart purposes + IOprint("Saving " .. DM .. " to " .. old_DM) + os.execute("mv " .. DM .. " " .. old_DM) + elseif NEB:file_exists(DM) then + IOprint("Deleting " .. DM .. " for a clean restart...") + os.execute("rm " .. DM) + end + + if NEB:file_exists(current_DM) then + IOprint("Deleting " .. DM .. " for a clean restart...") + os.execute("rm " .. DM) + IOprint("Restoring " .. current_DM .. " to " .. DM) + os.execute("cp " .. current_DM .. " " .. DM) + end + +end + +function stress_to_voigt(stress) + local voigt = flos.Array.empty(6) + voigt[1]=stress[1][1] + voigt[2]=stress[2][2] + voigt[3]=stress[3][3] + voigt[4]=(stress[2][3]+stress[3][2])*0.5 + voigt[5]=(stress[1][3]+stress[3][1])*0.5 + voigt[6]=(stress[1][2]+stress[2][1])*0.5 + return voigt +end +function siesta_update_xyz(current) + if not siesta.IONode then + -- only allow the IOnode to perform stuff... + return + end + local xyz_label = f_label_xyz ..tostring(current)..".xyz" + --self:_n_images=self.n_images + --self:_check_image(image) + + local f=io.open(xyz_label,"w") + f:write(tostring(#NEB[current].R).."\n \n") + --f:write(tostring(initialize:self.n_images).."\n \n") + for i=1,#NEB[current].R do + f:write(string.format(" %19.17f",tostring(NEB[current].R[i][1])).. " "..string.format("%19.17f",tostring(NEB[current].R[i][2]))..string.format(" %19.17f",tostring(NEB[current].R[i][3])).."\n") + end + f:close() + -- +end + +function siesta_update_xyz_vec(current) + if not siesta.IONode then + -- only allow the IOnode to perform stuff... + return + end + local xyz_vec_label = f_label_xyz_vec ..tostring(current)..".xyz" + --self:_n_images=self.n_images + --self:_check_image(image) + + local f=io.open(xyz_vec_label,"w") + f:write(tostring(#VCNEB[current].R).."\n \n") + --f:write(tostring(initialize:self.n_images).."\n \n") + for i=1,#VCNEB[current].R do + f:write(string.format(" %19.17f",tostring(VCNEB[current].R[i][1])).. " "..string.format("%19.17f",tostring(VCNEB[current].R[i][2]))..string.format(" %19.17f",tostring(VCNEB[current].R[i][3])).."\n") + end + f:close() + -- +end diff --git a/flos/special/backup-vcneb.lua b/flos/special/backup-vcneb.lua new file mode 100644 index 0000000..544fbf3 --- /dev/null +++ b/flos/special/backup-vcneb.lua @@ -0,0 +1,438 @@ +--- +-- NEB class +-- @classmod NEB + +local m = require "math" +local mc = require "flos.middleclass.middleclass" + +local array = require "flos.num" +local ferror = require "flos.error" +local error = ferror.floserr +local _NEB = require "flos.special.neb" + +-- Create the NEB class (inheriting the Optimizer construct) +local VCNEB = mc.class("VCNEB", _NEB) +--- Instantiating a new VCNEB` object. +function VCNEB:initialize(images,tbl) + -- Convert the remaining arguments to a table + local tbl = tbl or {} + -- Copy all images over + local size_img = #images[1].R + for i = 1, #images do + self[i-1] = images[i] + self.zeros=images[i].R- images[i].R + if #images[i].R ~= size_img then + error("VCNEB: images does not have same size of geometries!") + end + end + -- store the number of images (without the initial and final) + self.n_images = #images - 2 + -- This is _bad_ practice, however, + -- the middleclass system does not easily enable overwriting + -- the __index function (because it uses it) + self.initial = images[1] + self.final = images[#images] + --self.neb_type = "TDCINEB" --working + --============================================== + -- Defining NEB Type + --============================================== + local nt= tbl.neb_type + if nt == nil then + self.neb_type="VCCINEB" + else + self.neb_type = nt + end + --self.neb_type = "VCCINEB" + --============================================== + -- Defining VCNEB Label + --============================================== + self.DM_label="MgO-3x3x1-2V" + --============================================== + -- Defining VCNEB Temperature + --============================================== + -- For Adding Temperature Dependet + local nk =tbl.neb_temp + if nk == nil then + self.neb_temp = 0.0 + else + self.neb_temp= nk + end + self.boltzman=8.617333262*10^(-5) + self.beta=1.0/(self.neb_temp*self.boltzman) + --============================================== + -- Defining Number of Climing Image + --============================================== + --self.old_DM_label="" + --self.current_DM_label="" + -- an integer that describes when the climbing image + -- may be used, make large enough to never set it + local cl = tbl.climbing or 5 + if cl == false then + self._climbing = 1000000000000 + elseif cl == true then + -- We use the default value + self._climbing = 5 + else + -- Counter for climbing + self._climbing = cl + end + -- Set the climbing energy tolerance + self.climbing_tol = tbl.climbing_tol or 0.005 -- if the input is in eV/Ang this is 5 meV + self.niter = 0 + --============================================== + -- Defining spring Constant + --============================================== + -- One should also attach the spring-constant + -- It currently defaults to 5 + local kl = tbl.k or 10 + if type(kl) == "table" then + self.k = kl + else + self.k = setmetatable({}, + { + __index = function(t, k) + return kl + end + }) + end + self:init_files() +end +--- Calculate the tangent of a given image +-- @int image the image to calculate the tangent of +-- @return tangent force +-- The Tangent Edited for VCNEB +-- In case of VCNEB started with the same unit vectors the it should consistent +function VCNEB:tangent(image) + self:_check_image(image) + -- Determine energies of relevant images + local E_prev = self[image-1].E + local E_this = self[image].E + local E_next = self[image+1].E + -- Determine position differences + local dR_prev = self:dR(image-1, image) + local dR_next = self:dR(image, image+1) + local dR_this = self:dR(image, image) + -- Returned value + local tangent + -- Determine relevant energy scenario + --if dR_next:norm(0) == 0.0 or dR_prev:norm(0)==0.0 or dR_this:norm(0)==0.0 then + -- tangent = dR_this + -- return tangent + if E_next > E_this and E_this > E_prev then + tangent = dR_next + if dR_next:norm(0) == 0.0 then + return tangent + else + return tangent / tangent:norm(0) + end + elseif E_next < E_this and E_this < E_prev then + tangent = dR_prev + if dR_prev:norm(0)==0.0 then + return tangent + else + return tangent / tangent:norm(0) + end + else + -- We are at extremum, so mix + local dEmax = m.max( m.abs(E_next - E_this), m.abs(E_prev - E_this) ) + local dEmin = m.min( m.abs(E_next - E_this), m.abs(E_prev - E_this) ) + if E_next > E_prev then + tangent = dR_next * dEmax + dR_prev * dEmin + if dR_next:norm(0) == 0.0 or dR_prev:norm(0)==0.0 then + return tangent + else + return tangent / tangent:norm(0) + end + else + tangent = dR_next * dEmin + dR_prev * dEmax + if dR_next:norm(0) == 0.0 or dR_prev:norm(0)==0.0 then + return tangent + else + return tangent / tangent:norm(0) + end + end + end + -- At this point we have a tangent, + -- now normalize and return it + + --return tangent / tangent:norm(0) + --end +end + +--- Calculate the spring force of a given image +-- @int image the image to calculate the spring force of +-- @return spring force +-- function NEB:spring_force(image) +-- self:_check_image(image) + -- Determine position norms +-- local dR_prev = self:dR(image-1, image):norm(0) +-- local dR_next = self:dR(image, image+1):norm(0) + -- Set spring force as F = k (R1-R2) * tangent + --if dR_prev==0.0 or dR_next==0.0 then + -- return self:tangent(image) --self.k[image] * (dR_next - dR_prev) * self:tangent(image) + --else + -- return self.k[image] * (dR_next - dR_prev) * self:tangent(image) + --end +--end + + + +--- Calculate the perpendicular force of a given image +-- @int image the image to calculate the perpendicular force of +-- @return perpendicular force +-- Edited to adopt the VCNEB +function VCNEB:perpendicular_force(image) + self:_check_image(image) + if self:tangent(image):norm(0)==0.0 then + return self[image].F + else + -- Subtract the force projected onto the tangent to get the perpendicular force + local P = self[image].F:project(self:tangent(image)) + return self[image].F - P --self:tangent(image) + end +end +--- Calculate the curvature of the force with regards to the tangent +-- @int image the image to calculate the curvature of + + + +function VCNEB:neb_force(image) + self:_check_image(image) + local NEB_F + local DNEB_F + local TDNEB_F + -- Only run Climbing image after a certain amount of steps (robustness) + -- Typically this number is 5. + --=================================================================== + --Adding Variable Cell Climing Image Nudged Elastic Band + --=================================================================== + if self.neb_type == "VCCINEB" then + if self.niter > self._climbing and self:climbing(image) then + local F = self[image].F + NEB_F = F - 2 * F:project( self:tangent(image) ) + else + DNEB_F = 0.0 + NEB_F = self:perpendicular_force(image) + self:spring_force(image) + DNEB_F + end + return NEB_F + end + --=================================================================== + --Adding Variable Cell Climing Image-Double Nudged Elastic Band + --=================================================================== + if self.neb_type == "VCCIDNEB" then + if self.niter > self._climbing and self:climbing(image) then + local F = self[image].F + if self:tangent(image):norm(0)==0.0 then + NEB_F = F + else + NEB_F = F - 2 * F:project( self:tangent(image) ) + end + else + DNEB_F = self:perpendicular_spring_force(image)-self:perpendicular_spring_force(image):project(self:perpendicular_force(image))*(self:perpendicular_force(image)) + NEB_F = self:perpendicular_force(image) + self:spring_force(image) + DNEB_F--+ self:perpendicular_spring_force(image)-self:perpendicular_spring_force(image):project(self:perpendicular_force(image))*(self:perpendicular_force(image)) --+DNEB_F + --print (DNEB_F) + end + return NEB_F + end + --=================================================================== + --Adding Temperature Dependent Climing Image-Nudged Elastic Band + --=================================================================== + if self.neb_type == "TDVCCINEB" then + if self.niter > self._climbing and self:climbing(image) then + local F = self[image].F + if self:tangent(image):norm(0)==0.0 then + NEB_F = F + else + NEB_F = F - 2 * F:project( self:tangent(image) ) + end + else + TDNEB_F = self:perpendicular_force(image)-(self:curvature(image)/self.beta) + NEB_F = TDNEB_F + self:spring_force(image) + end + return NEB_F + end +end +--- Query the current force (same as `NEB:force` but with IO included) +-- @int image the image +-- @return force +function VCNEB:force(image, IO) + self:_check_image(image) + if image == 1 then + -- Increment step-counter + self.niter = self.niter + 1 + end + local F = self[image].F + local tangent = self:tangent(image) + local perp_F = self:perpendicular_force(image) + local spring_F = self:spring_force(image) + local NEB_F = self:neb_force(image) + -- Things I want to output in files as control (all in 3xN format) + if IO then + local f + -- Current coordinates (ie .R) + f = io.open( ("VCNEB.%d.R"):format(image), "a") + self[image].R:savetxt(f) + f:close() + -- Forces before (ie .F) + f = io.open( ("VCNEB.%d.F"):format(image), "a") + F:savetxt(f) + f:close() + -- Perpendicular force + f = io.open( ("VCNEB.%d.F.P"):format(image), "a") + perp_F:savetxt(f) + f:close() + -- Spring force + f = io.open( ("VCNEB.%d.F.S"):format(image), "a") + spring_F:savetxt(f) + f:close() + -- NEB Force + f = io.open( ("VCNEB.%d.F.NEB"):format(image), "a") + NEB_F:savetxt(f) + f:close() + -- Tangent + f = io.open( ("VCNEB.%d.T"):format(image), "a") + tangent:savetxt(f) + f:close() + -- dR - previous reaction coordinate + f = io.open( ("VCNEB.%d.dR_prev"):format(image), "a") + self:dR(image-1, image):savetxt(f) + f:close() + -- dR - next reaction coordinate + f = io.open( ("VCNEB.%d.dR_next"):format(image), "a") + self:dR(image, image+1):savetxt(f) + f:close() + end + -- Fake return to test + return NEB_F +end +--- Store the current step of the NEB iteration with the appropriate results +function VCNEB:save(IO) + -- If we should not do IO, return immediately + if not IO then + return + end + -- local E0 + local E0 = self[0].E + -- Now setup the matrix to write the NEB-results + local dat = array.Array( self.n_images + 2, 6) + for i = 0, self.n_images + 1 do + local row = dat[i+1] + -- image number (0 for initial, n_images + 1 for final) + row[1] = i + -- Accumulated reaction coordinate + if i == 0 then + row[2] = 0. + else + row[2] = dat[i][2] + self:dR(i-1, i):norm(0) + end + -- Total energy of current iteration + row[3] = self[i].E + -- Energy difference from initial image + row[4] = self[i].E - E0 + -- Image curvature + if i == 0 or i == self.n_images + 1 then + row[5] = 0. + else + row[5] = self:curvature(i) + end + -- Vector-norm of maximum force of the NEB-force + if i == 0 or i == self.n_images + 1 then + row[6] = 0. + else + row[6] = self:neb_force(i):norm():max() + end + end + local f = io.open("VCNEB.results", "a") + dat:savetxt(f) + f:close() +end + +--- Initialize all files that will be written to +function VCNEB:init_files() + -- We clean all image data for a new run + local function new_file(fname, ...) + local f = io.open(fname, 'w') + local a = {...} + for _, v in pairs(a) do + f:write("# " .. v .. "\n") + end + f:close() + end + new_file("VCNEB.results", "NEB results file", + "Image reaction-coordinate Energy E-diff Curvature F-max(atom)") + for img = 1, self.n_images do + new_file( ("VCNEB.%d.R"):format(img), "Coordinates") + new_file( ("VCNEB.%d.F"):format(img), "Constrained force") + new_file( ("VCNEB.%d.F.P"):format(img), "Perpendicular force") + new_file( ("VCNEB.%d.F.S"):format(img), "Spring force") + new_file( ("VCNEB.%d.F.NEB"):format(img), "Resulting NEB force") + new_file( ("VCNEB.%d.T"):format(img), "NEB tangent") + new_file( ("VCNEB.%d.dR_prev"):format(img), "Reaction distance (previous)") + new_file( ("VCNEB.%d.dR_next"):format(img), "Reaction distance (next)") + end +end +--- Print to screen some information regarding the NEB algorithm +function VCNEB:info() + if self.neb_type=="VCCINEB" then + --if neb_type=="VCCINEB" then + print ("============================================") + print (" The Variable Cell CI-NEB (VCCINEB) method ") + print ("============================================") + elseif self.neb_type == "VCCIDNEB" then + print ("=============================================") + print (" The Variable Cell CI-DNEB (VCCIDNEB) Method ") + print ("=============================================") + elseif self.neb_type == "TDVCCINEB" then + print ("=================================================") + print (" The Temperature Dependent CI-DNEB(VCDNEB) Method ") + print ("=================================================") + print ("The Temperature is : ".. self.neb_temp .. " K") + end + print("VCNEB has " .. self.n_images) + print("VCNEB uses climbing after " .. self._climbing .. " steps") + local tmp = array.Array( self.n_images + 1 ) + tmp[1] = self:dR(0, 1):norm(0) + for i = 2, self.n_images + 1 do + tmp[i] = tmp[i-1] + self:dR(i-1, i):norm(0) + end + print("VCNEB reaction coordinates: ") + print(tostring(tmp)) + local tmp = array.Array( self.n_images ) + for i = 1, self.n_images do + tmp[i] = self.k[i] + end + print("VCNEB spring constant: ") + print(tostring(tmp)) +end +-- Calculatin Perpendicular Spring force +function VCNEB:perpendicular_spring_force(image) + self:_check_image(image) + if self:tangent(image):norm(0)==0.0 then + return self:spring_force(image) + else + local PS=self:spring_force(image):project(self:tangent(image)) + return self:spring_force(image)-PS + end +end +function VCNEB:file_exists(name)--name + --local name + --DM_name=tostring(name) + DM_name=name + --print ("DM_name is :" .. DM_name) + local check + --local DM_name = name + local f = io.open(DM_name, "r") --name + if f ~= nil then + io.close(f) + --check=true + --print("TRUE: The file ".. DM_name.. " Exist!") + return true + else + --print("False: The file ".. DM_name.. " Doesn't Exist!") + return false + --check=false + end + --return check +end + +return VCNEB diff --git a/flos/special/dneb.lua b/flos/special/dneb.lua index ead1cb8..c0eaaf4 100644 --- a/flos/special/dneb.lua +++ b/flos/special/dneb.lua @@ -4,6 +4,7 @@ local mc = require "flos.middleclass.middleclass" local _NEB = require "flos.special.neb" +local array = require "flos.num" -- Create the D-NEB class local DNEB = mc.class("DNEB", _NEB) @@ -44,4 +45,143 @@ function DNEB:neb_force(image) return NEB_F + PS_F - PS_F:project( P_F ) * P_F end + +--- Print to screen some information regarding the NEB algorithm +function DNEB:info() + print("DNEB Number of Images : " .. self.n_images) + print("DNEB Use Climbing After : " .. self._climbing .. " Steps") + local tmp = array.Array( self.n_images + 1 ) + --tmp[1] = self:dR(0, 1):norm(0) + tmp[1] = self:dR(0, 1):norm(0) + for i = 2, self.n_images + 1 do + tmp[i] = tmp[i-1] + self:dR(i-1, i):norm(0) + end + print("DNEB Reaction Coordinates: ") + print(tostring(tmp)) + local tmp = array.Array( self.n_images ) + for i = 1, self.n_images do + tmp[i] = self.k[i] + end + print("DNEB spring constant: ") + print(tostring(tmp)) +end + + +function DNEB:force(image, IO) + self:_check_image(image) + + if image == 1 then + -- Increment step-counter + self.niter = self.niter + 1 + end + + local NEB_F = self:neb_force(image) + + -- Things I want to output in files as control (all in 3xN format) + if IO then + local f + + -- Current coordinates (ie .R) + f = io.open( ("DNEB.%d.R"):format(image), "a") + self[image].R:savetxt(f) + f:close() + + -- Forces before (ie .F) + f = io.open( ("DNEB.%d.F"):format(image), "a") + self[image].F:savetxt(f) + f:close() + + -- Perpendicular force + f = io.open( ("DNEB.%d.F.P"):format(image), "a") + self:perpendicular_force(image):savetxt(f) + f:close() + + -- Spring force parallel + f = io.open( ("DNEB.%d.F.S.parallel"):format(image), "a") + self:spring_force(image):savetxt(f) + f:close() + + -- Spring force perdpendicular + f = io.open( ("DNEB.%d.F.S.perpendicular"):format(image), "a") + self:perpendicular_spring_force(image):savetxt(f) + f:close() + + -- NEB Force + f = io.open( ("DNEB.%d.F.NEB"):format(image), "a") + NEB_F:savetxt(f) + f:close() + + -- Tangent + f = io.open( ("DNEB.%d.T"):format(image), "a") + self:tangent(image):savetxt(f) + f:close() + + -- dR - previous reaction coordinate + f = io.open( ("DNEB.%d.dR_prev"):format(image), "a") + self:dR(image-1, image):savetxt(f) + f:close() + + -- dR - next reaction coordinate + f = io.open( ("DNEB.%d.dR_next"):format(image), "a") + self:dR(image, image+1):savetxt(f) + f:close() + + end + + -- Fake return to test + return NEB_F + +end + + +function DNEB:init_files() + + -- We clean all image data for a new run + local function new_file(fname, ...) + local f = io.open(fname, 'w') + local a = {...} + for _, v in pairs(a) do + f:write("# " .. v .. "\n") + end + f:close() + end + + new_file("DNEB.results", "DNEB results file", + "Image reaction-coordinate Energy E-diff Curvature F-max(atom)") + + for img = 1, self.n_images do + new_file( ("DNEB.%d.R"):format(img), "Coordinates") + new_file( ("DNEB.%d.F"):format(img), "Constrained force") + new_file( ("DNEB.%d.F.P"):format(img), "Perpendicular force") + new_file( ("DNEB.%d.F.S.parallel"):format(img), "Spring parallel force") + new_file( ("DNEB.%d.F.S.perpendicular"):format(img), "Spring perpendicular force") + new_file( ("DNEB.%d.F.NEB"):format(img), "Resulting NEB force") + new_file( ("DNEB.%d.T"):format(img), "NEB tangent") + new_file( ("DNEB.%d.dR_prev"):format(img), "Reaction distance (previous)") + new_file( ("DNEB.%d.dR_next"):format(img), "Reaction distance (next)") + end + +end + +function DNEB:file_exists(name)--name + --local name + --DM_name=tostring(name) + DM_name=name + --print ("DM_name is :" .. DM_name) + local check + --local DM_name = name + local f = io.open(DM_name, "r") --name + if f ~= nil then + io.close(f) + --check=true + --print("TRUE: The file ".. DM_name.. " Exist!") + return true + else + --print("False: The file ".. DM_name.. " Doesn't Exist!") + return false + --check=false + end + --return check +end + return DNEB diff --git a/flos/special/init.lua b/flos/special/init.lua index b11aff7..64c3ee6 100644 --- a/flos/special/init.lua +++ b/flos/special/init.lua @@ -9,5 +9,8 @@ local ret = {} ret.ForceHessian = require "flos.special.forcehessian" ret.NEB = require "flos.special.neb" ret.DNEB = require "flos.special.dneb" +ret.VCNEB = require "flos.special.vcneb" +ret.VCDNEB = require "flos.special.vcdneb" +ret.TNEB = require "flos.special.tneb" return ret diff --git a/flos/special/neb.lua b/flos/special/neb.lua index 606ce87..4d6db7b 100644 --- a/flos/special/neb.lua +++ b/flos/special/neb.lua @@ -547,4 +547,27 @@ function NEB:info() end + +function NEB:file_exists(name)--name + --local name + --DM_name=tostring(name) + DM_name=name + --print ("DM_name is :" .. DM_name) + local check + --local DM_name = name + local f = io.open(DM_name, "r") --name + if f ~= nil then + io.close(f) + --check=true + --print("TRUE: The file ".. DM_name.. " Exist!") + return true + else + --print("False: The file ".. DM_name.. " Doesn't Exist!") + return false + --check=false + end + --return check +end + + return NEB diff --git a/flos/special/tneb.lua b/flos/special/tneb.lua new file mode 100644 index 0000000..0bbfbbe --- /dev/null +++ b/flos/special/tneb.lua @@ -0,0 +1,324 @@ +--- +-- NEB class +-- @classmod NEB + +local m = require "math" +local mc = require "flos.middleclass.middleclass" + +local array = require "flos.num" +local ferror = require "flos.error" +local error = ferror.floserr +local _NEB = require "flos.special.neb" + +-- Create the NEB class (inheriting the Optimizer construct) +local TNEB = mc.class("TNEB", _NEB) +--- Instantiating a new TNEB` object. + --============================================== + -- Defining TNEB Temperature + --============================================== + -- For Adding Temperature Dependet +function TNEB:initialize(images,tbl) + -- Convert the remaining arguments to a table + local tbl = tbl or {} + -- Copy all images over + local size_img = #images[1].R + for i = 1, #images do + self[i-1] = images[i] + self.zeros=images[i].R- images[i].R + if #images[i].R ~= size_img then + error("TNEB: images does not have same size of geometries!") + end + end + -- store the number of images (without the initial and final) + self.n_images = #images - 2 + -- This is _bad_ practice, however, + -- the middleclass system does not easily enable overwriting + -- the __index function (because it uses it) + self.initial = images[1] + self.final = images[#images] + --self.neb_type = "TDCINEB" --working + --============================================== + -- Defining NEB Type + --============================================== + --local nt= tbl.neb_type + --if nt == nil then + -- self.neb_type="VCCINEB" + --else + -- self.neb_type = nt + --end + --self.neb_type = "VCCINEB" + --============================================== + -- Defining VCNEB Label + --============================================== + + --============================================== + -- Defining VCNEB Temperature + --============================================== + -- For Adding Temperature Dependet + local nk =tbl.neb_temp + if nk == nil then + self.neb_temp = 0.0 + else + self.neb_temp= nk + end + self.boltzman=8.617333262*10^(-5) + self.beta=1.0/(self.neb_temp*self.boltzman) + --============================================== + -- Defining Number of Climing Image + --============================================== + --self.old_DM_label="" + --self.current_DM_label="" + -- an integer that describes when the climbing image + -- may be used, make large enough to never set it + local cl = tbl.climbing or 5 + if cl == false then + self._climbing = 1000000000000 + elseif cl == true then + -- We use the default value + self._climbing = 5 + else + -- Counter for climbing + self._climbing = cl + end + -- Set the climbing energy tolerance + self.climbing_tol = tbl.climbing_tol or 0.005 -- if the input is in eV/Ang this is 5 meV + self.niter = 0 + --============================================== + -- Defining spring Constant + --============================================== + -- One should also attach the spring-constant + -- It currently defaults to 5 + local kl = tbl.k or 10 + if type(kl) == "table" then + self.k = kl + else + self.k = setmetatable({}, + { + __index = function(t, k) + return kl + end + }) + end + self:init_files() +end + + + + + +-- local nk =tbl.neb_temp +-- if nk == nil then +-- self.neb_temp = 0.0 +-- else +-- self.neb_temp= nk +-- end +-- self.boltzman=8.617333262*10^(-5) +-- self.beta=1.0/(self.neb_temp*self.boltzman) + + +--- Calculate the tangent of a given image +-- @int image the image to calculate the tangent of +-- @return tangent force +--- Calculate the perpendicular force of a given image +-- @int image the image to calculate the perpendicular force of +-- @return perpendicular force +-- Edited to adopt the VCNEB +--- Calculate the curvature of the force with regards to the tangent +-- @int image the image to calculate the curvature of + +function TNEB:neb_force(image) + self:_check_image(image) + local NEB_F + local TDNEB_F + -- Only run Climbing image after a certain amount of steps (robustness) + -- Typically this number is 5. + --=================================================================== + --Adding Temperature Dependent Climing Image-Nudged Elastic Band + --=================================================================== + if self.niter > self._climbing and self:climbing(image) then + local F = self[image].F + if self:tangent(image):norm(0)==0.0 then + NEB_F = F + else + NEB_F = F - 2 * F:project( self:tangent(image) ) + end + else + --NEB_NORM = F - self:perpendicular_force(image) + TDNEB_F = self:perpendicular_force(image)-(self:curvature(image)/self.beta) * NEB_NORM + NEB_F = TDNEB_F + self:spring_force(image) + end + return NEB_F + end +--- Query the current force (same as `NEB:force` but with IO included) +-- @int image the image +-- @return force +function TNEB:force(image, IO) + self:_check_image(image) + if image == 1 then + -- Increment step-counter + self.niter = self.niter + 1 + end + local F = self[image].F + local tangent = self:tangent(image) + local perp_F = self:perpendicular_force(image) + local spring_F = self:spring_force(image) + local NEB_F = self:neb_force(image) + -- Things I want to output in files as control (all in 3xN format) + if IO then + local f + -- Current coordinates (ie .R) + f = io.open( ("TNEB.%d.R"):format(image), "a") + self[image].R:savetxt(f) + f:close() + -- Forces before (ie .F) + f = io.open( ("TNEB.%d.F"):format(image), "a") + F:savetxt(f) + f:close() + -- Perpendicular force + f = io.open( ("TNEB.%d.F.P"):format(image), "a") + perp_F:savetxt(f) + f:close() + -- Spring force + f = io.open( ("TNEB.%d.F.S"):format(image), "a") + spring_F:savetxt(f) + f:close() + -- NEB Force + f = io.open( ("TNEB.%d.F.NEB"):format(image), "a") + NEB_F:savetxt(f) + f:close() + -- Tangent + f = io.open( ("TNEB.%d.T"):format(image), "a") + tangent:savetxt(f) + f:close() + -- dR - previous reaction coordinate + f = io.open( ("TNEB.%d.dR_prev"):format(image), "a") + self:dR(image-1, image):savetxt(f) + f:close() + -- dR - next reaction coordinate + f = io.open( ("TNEB.%d.dR_next"):format(image), "a") + self:dR(image, image+1):savetxt(f) + f:close() + end + -- Fake return to test + return NEB_F +end +--- Store the current step of the NEB iteration with the appropriate results +function TNEB:save(IO) + -- If we should not do IO, return immediately + if not IO then + return + end + -- local E0 + local E0 = self[0].E + -- Now setup the matrix to write the NEB-results + local dat = array.Array( self.n_images + 2, 6) + for i = 0, self.n_images + 1 do + local row = dat[i+1] + -- image number (0 for initial, n_images + 1 for final) + row[1] = i + -- Accumulated reaction coordinate + if i == 0 then + row[2] = 0. + else + row[2] = dat[i][2] + self:dR(i-1, i):norm(0) + end + -- Total energy of current iteration + row[3] = self[i].E + -- Energy difference from initial image + row[4] = self[i].E - E0 + -- Image curvature + if i == 0 or i == self.n_images + 1 then + row[5] = 0. + else + row[5] = self:curvature(i) + end + -- Vector-norm of maximum force of the NEB-force + if i == 0 or i == self.n_images + 1 then + row[6] = 0. + else + row[6] = self:neb_force(i):norm():max() + end + end + local f = io.open("TNEB.results", "a") + dat:savetxt(f) + f:close() +end + +--- Initialize all files that will be written to +function TNEB:init_files() + -- We clean all image data for a new run + local function new_file(fname, ...) + local f = io.open(fname, 'w') + local a = {...} + for _, v in pairs(a) do + f:write("# " .. v .. "\n") + end + f:close() + end + new_file("TNEB.results", "NEB results file", + "Image reaction-coordinate Energy E-diff Curvature F-max(atom)") + for img = 1, self.n_images do + new_file( ("TNEB.%d.R"):format(img), "Coordinates") + new_file( ("TNEB.%d.F"):format(img), "Constrained force") + new_file( ("TNEB.%d.F.P"):format(img), "Perpendicular force") + new_file( ("TNEB.%d.F.S"):format(img), "Spring force") + new_file( ("TNEB.%d.F.NEB"):format(img), "Resulting NEB force") + new_file( ("TNEB.%d.T"):format(img), "NEB tangent") + new_file( ("TNEB.%d.dR_prev"):format(img), "Reaction distance (previous)") + new_file( ("TNEB.%d.dR_next"):format(img), "Reaction distance (next)") + end +end +--- Print to screen some information regarding the NEB algorithm +function TNEB:info() + print ("=================================================") + print (" The Temperature Dependent CI-DNEB(VCDNEB) Method ") + print ("=================================================") + print ("The Temperature is : ".. self.neb_temp .. " K") + print("TNEB has " .. self.n_images) + print("TNEB uses climbing after " .. self._climbing .. " steps") + local tmp = array.Array( self.n_images + 1 ) + tmp[1] = self:dR(0, 1):norm(0) + for i = 2, self.n_images + 1 do + tmp[i] = tmp[i-1] + self:dR(i-1, i):norm(0) + end + print("TNEB reaction coordinates: ") + print(tostring(tmp)) + local tmp = array.Array( self.n_images ) + for i = 1, self.n_images do + tmp[i] = self.k[i] + end + print("TNEB spring constant: ") + print(tostring(tmp)) +end +-- Calculatin Perpendicular Spring force +function TNEB:perpendicular_spring_force(image) + self:_check_image(image) + if self:tangent(image):norm(0)==0.0 then + return self:spring_force(image) + else + local PS=self:spring_force(image):project(self:tangent(image)) + return self:spring_force(image)-PS + end +end +function TNEB:file_exists(name)--name + --local name + --DM_name=tostring(name) + DM_name=name + --print ("DM_name is :" .. DM_name) + local check + --local DM_name = name + local f = io.open(DM_name, "r") --name + if f ~= nil then + io.close(f) + --check=true + --print("TRUE: The file ".. DM_name.. " Exist!") + return true + else + --print("False: The file ".. DM_name.. " Doesn't Exist!") + return false + --check=false + end + --return check +end + +return TNEB diff --git a/flos/special/vcdneb.lua b/flos/special/vcdneb.lua new file mode 100644 index 0000000..d0b542f --- /dev/null +++ b/flos/special/vcdneb.lua @@ -0,0 +1,234 @@ +--- +-- VCDNEB class +-- @classmod VC-DNEB + +local m = require "math" +local mc = require "flos.middleclass.middleclass" + +local array = require "flos.num" +local ferror = require "flos.error" +local error = ferror.floserr +local _NEB = require "flos.special.vcneb" + +-- Create the NEB class (inheriting the Optimizer construct) +local VCDNEB = mc.class("VCDNEB", _NEB) +--- Instantiating a new VCNEB` object. + +--- Calculate the tangent of a given image +-- @int image the image to calculate the tangent of +-- @return tangent force +-- The Tangent Edited for VC-DNEB +-- In case of VC-DNEB started with the same unit vectors the it should consistent + +--- Calculate the spring force of a given image +-- @int image the image to calculate the spring force of +-- @return spring force +--- Calculate the curvature of the force with regards to the tangent +-- @int image the image to calculate the curvature of + +--- Calculate perpendicular spring force for a given image +-- @int image image to calculate the perpendicular spring force of +-- @return the perpendicular spring force +function VCDNEB:perpendicular_spring_force(image) + -- We don't need to check image (these function calls does exactly that) + local S_F = self:spring_force(image) + + -- Return the new perpendicular spring force + return S_F - S_F:project( self:tangent(image) ) +end + +function VCDNEB:neb_force(image) + -- Calculate *original* NEB force + local NEB_F = _NEB.neb_force(self, image) + + -- Only correct in case we are past climbing + if self.niter > self._climbing and self:climbing(image) then + return NEB_F + end + + local PS_F = self:perpendicular_spring_force(image) + local P_F = self:perpendicular_force(image) + + -- This is equivalent to: + -- flatdot(PS_F, P_F) / norm(P_F)^2 * P_F .* P_F + -- with .* being the elementwise multiplication + return NEB_F + PS_F - PS_F:project( P_F ) * P_F +end + +--- Query the current force (same as `NEB:force` but with IO included) +-- @int image the image +-- @return force +function VCDNEB:force(image, IO) + self:_check_image(image) + if image == 1 then + -- Increment step-counter + self.niter = self.niter + 1 + end + local F = self[image].F + local tangent = self:tangent(image) + local perp_F = self:perpendicular_force(image) + local spring_F = self:spring_force(image) + local NEB_F = self:neb_force(image) + -- Things I want to output in files as control (all in 3xN format) + if IO then + local f + -- Current coordinates (ie .R) + f = io.open( ("VCDNEB.%d.R"):format(image), "a") + self[image].R:savetxt(f) + f:close() + -- Forces before (ie .F) + f = io.open( ("VCDNEB.%d.F"):format(image), "a") + F:savetxt(f) + f:close() + -- Perpendicular force + f = io.open( ("VCDNEB.%d.F.P"):format(image), "a") + perp_F:savetxt(f) + f:close() + -- Spring force + f = io.open( ("VCDNEB.%d.F.S"):format(image), "a") + spring_F:savetxt(f) + f:close() + -- NEB Force + f = io.open( ("VCDNEB.%d.F.NEB"):format(image), "a") + NEB_F:savetxt(f) + f:close() + -- Tangent + f = io.open( ("VCDNEB.%d.T"):format(image), "a") + tangent:savetxt(f) + f:close() + -- dR - previous reaction coordinate + f = io.open( ("VCDNEB.%d.dR_prev"):format(image), "a") + self:dR(image-1, image):savetxt(f) + f:close() + -- dR - next reaction coordinate + f = io.open( ("VCDNEB.%d.dR_next"):format(image), "a") + self:dR(image, image+1):savetxt(f) + f:close() + end + -- Fake return to test + return NEB_F +end +--- Store the current step of the NEB iteration with the appropriate results +function VCDNEB:save(IO) + -- If we should not do IO, return immediately + if not IO then + return + end + -- local E0 + local E0 = self[0].E + -- Now setup the matrix to write the NEB-results + local dat = array.Array( self.n_images + 2, 6) + for i = 0, self.n_images + 1 do + local row = dat[i+1] + -- image number (0 for initial, n_images + 1 for final) + row[1] = i + -- Accumulated reaction coordinate + if i == 0 then + row[2] = 0. + else + row[2] = dat[i][2] + self:dR(i-1, i):norm(0) + end + -- Total energy of current iteration + row[3] = self[i].E + -- Energy difference from initial image + row[4] = self[i].E - E0 + -- Image curvature + if i == 0 or i == self.n_images + 1 then + row[5] = 0. + else + row[5] = self:curvature(i) + end + -- Vector-norm of maximum force of the NEB-force + if i == 0 or i == self.n_images + 1 then + row[6] = 0. + else + row[6] = self:neb_force(i):norm():max() + end + end + local f = io.open("VCDNEB.results", "a") + dat:savetxt(f) + f:close() +end + +--- Initialize all files that will be written to +function VCDNEB:init_files() + -- We clean all image data for a new run + local function new_file(fname, ...) + local f = io.open(fname, 'w') + local a = {...} + for _, v in pairs(a) do + f:write("# " .. v .. "\n") + end + f:close() + end + new_file("VCDNEB.results", "NEB results file", + "Image reaction-coordinate Energy E-diff Curvature F-max(atom)") + for img = 1, self.n_images do + new_file( ("VCDNEB.%d.R"):format(img), "Coordinates") + new_file( ("VCDNEB.%d.F"):format(img), "Constrained force") + new_file( ("VCDNEB.%d.F.P"):format(img), "Perpendicular force") + new_file( ("VCDNEB.%d.F.S"):format(img), "Spring force") + new_file( ("VCDNEB.%d.F.NEB"):format(img), "Resulting NEB force") + new_file( ("VCDNEB.%d.T"):format(img), "NEB tangent") + new_file( ("VCDNEB.%d.dR_prev"):format(img), "Reaction distance (previous)") + new_file( ("VCDNEB.%d.dR_next"):format(img), "Reaction distance (next)") + end +end +--- Print to screen some information regarding the NEB algorithm +function VCDNEB:info() +-- print (************************** End: TS CHECKS AND WARNINGS **************************) + print ("***************** The Variable Cell Double NEB Method *******************") + + --print ("============================================") + --print (" The Variable Cell Double NEB Method ") + --print ("============================================") + + + print("VC-DNEB Number of Images : " .. self.n_images) + print("VC-DNEB Use Climbing After :" .. self._climbing .. " Steps") + local tmp = array.Array( self.n_images + 1 ) + tmp[1] = self:dR(0, 1):norm(0) + for i = 2, self.n_images + 1 do + tmp[i] = tmp[i-1] + self:dR(i-1, i):norm(0) + end + print("VC-DNEB Reaction Coordinates: ") + print(tostring(tmp)) + local tmp = array.Array( self.n_images ) + for i = 1, self.n_images do + tmp[i] = self.k[i] + end + print("VC-DNEB Cpring Constant: ") + print(tostring(tmp)) +end +-- Calculatin Perpendicular Spring force +function VCDNEB:perpendicular_spring_force(image) + self:_check_image(image) + if self:tangent(image):norm(0)==0.0 then + return self:spring_force(image) + else + local PS=self:spring_force(image):project(self:tangent(image)) + return self:spring_force(image)-PS + end +end +function VCDNEB:file_exists(name)--name + --local name + --DM_name=tostring(name) + DM_name=name + --print ("DM_name is :" .. DM_name) + local check + --local DM_name = name + local f = io.open(DM_name, "r") --name + if f ~= nil then + io.close(f) + --check=true + --print("TRUE: The file ".. DM_name.. " Exist!") + return true + else + --print("False: The file ".. DM_name.. " Doesn't Exist!") + return false + --check=false + end + --return check +end + +return VCDNEB diff --git a/flos/special/vcneb.lua b/flos/special/vcneb.lua new file mode 100644 index 0000000..8c20718 --- /dev/null +++ b/flos/special/vcneb.lua @@ -0,0 +1,358 @@ +--- +-- NEB class +-- @classmod NEB + +local m = require "math" +local mc = require "flos.middleclass.middleclass" + +local array = require "flos.num" +local ferror = require "flos.error" +local error = ferror.floserr +local _NEB = require "flos.special.neb" + +-- Create the NEB class (inheriting the Optimizer construct) +local VCNEB = mc.class("VCNEB", _NEB) +--- Instantiating a new VCNEB` object. +function VCNEB:initialize(images,tbl) + -- Convert the remaining arguments to a table + local tbl = tbl or {} + -- Copy all images over + local size_img = #images[1].R + for i = 1, #images do + self[i-1] = images[i] + self.zeros=images[i].R- images[i].R + if #images[i].R ~= size_img then + error("VCNEB: images does not have same size of geometries!") + end + end + -- store the number of images (without the initial and final) + self.n_images = #images - 2 + -- This is _bad_ practice, however, + -- the middleclass system does not easily enable overwriting + -- the __index function (because it uses it) + self.initial = images[1] + self.final = images[#images] + -- an integer that describes when the climbing image + -- may be used, make large enough to never set it + local cl = tbl.climbing or 5 + if cl == false then + self._climbing = 1000000000000 + elseif cl == true then + -- We use the default value + self._climbing = 5 + else + -- Counter for climbing + self._climbing = cl + end + -- Set the climbing energy tolerance + self.climbing_tol = tbl.climbing_tol or 0.005 -- if the input is in eV/Ang this is 5 meV + self.niter = 0 + --============================================== + -- Defining spring Constant + --============================================== + -- One should also attach the spring-constant + -- It currently defaults to 5 + local kl = tbl.k or 10 + if type(kl) == "table" then + self.k = kl + else + self.k = setmetatable({}, + { + __index = function(t, k) + return kl + end + }) + end + self:init_files() +end +--- Calculate the tangent of a given image +-- @int image the image to calculate the tangent of +-- @return tangent force +-- The Tangent Edited for VCNEB +-- In case of VCNEB started with the same unit vectors the it should consistent +function VCNEB:tangent(image) + self:_check_image(image) + -- Determine energies of relevant images + local E_prev = self[image-1].E + local E_this = self[image].E + local E_next = self[image+1].E + -- Determine position differences + local dR_prev = self:dR(image-1, image) + local dR_next = self:dR(image, image+1) + local dR_this = self:dR(image, image) + -- Returned value + local tangent + -- Determine relevant energy scenario + --if dR_next:norm(0) == 0.0 or dR_prev:norm(0)==0.0 or dR_this:norm(0)==0.0 then + -- tangent = dR_this + -- return tangent + if E_next > E_this and E_this > E_prev then + tangent = dR_next + if dR_next:norm(0) == 0.0 then + return tangent + else + return tangent / tangent:norm(0) + end + elseif E_next < E_this and E_this < E_prev then + tangent = dR_prev + if dR_prev:norm(0)==0.0 then + return tangent + else + return tangent / tangent:norm(0) + end + else + -- We are at extremum, so mix + local dEmax = m.max( m.abs(E_next - E_this), m.abs(E_prev - E_this) ) + local dEmin = m.min( m.abs(E_next - E_this), m.abs(E_prev - E_this) ) + if E_next > E_prev then + tangent = dR_next * dEmax + dR_prev * dEmin + if dR_next:norm(0) == 0.0 or dR_prev:norm(0)==0.0 then + return tangent + else + return tangent / tangent:norm(0) + end + else + tangent = dR_next * dEmin + dR_prev * dEmax + if dR_next:norm(0) == 0.0 or dR_prev:norm(0)==0.0 then + return tangent + else + return tangent / tangent:norm(0) + end + end + end + -- At this point we have a tangent, + -- now normalize and return it + + --return tangent / tangent:norm(0) + --end +end + +--- Calculate the spring force of a given image +-- @int image the image to calculate the spring force of +-- @return spring force +-- function NEB:spring_force(image) +-- self:_check_image(image) + -- Determine position norms +-- local dR_prev = self:dR(image-1, image):norm(0) +-- local dR_next = self:dR(image, image+1):norm(0) + -- Set spring force as F = k (R1-R2) * tangent + --if dR_prev==0.0 or dR_next==0.0 then + -- return self:tangent(image) --self.k[image] * (dR_next - dR_prev) * self:tangent(image) + --else + -- return self.k[image] * (dR_next - dR_prev) * self:tangent(image) + --end +--end + + + +--- Calculate the perpendicular force of a given image +-- @int image the image to calculate the perpendicular force of +-- @return perpendicular force +-- Edited to adopt the VCNEB +function VCNEB:perpendicular_force(image) + self:_check_image(image) + if self:tangent(image):norm(0)==0.0 then + return self[image].F + else + -- Subtract the force projected onto the tangent to get the perpendicular force + local P = self[image].F:project(self:tangent(image)) + return self[image].F - P --self:tangent(image) + end +end +--- Calculate the curvature of the force with regards to the tangent +-- @int image the image to calculate the curvature of + + + +function VCNEB:neb_force(image) + self:_check_image(image) + local NEB_F + local DNEB_F + local TDNEB_F + -- Only run Climbing image after a certain amount of steps (robustness) + -- Typically this number is 5. + --=================================================================== + --Adding Variable Cell Climing Image Nudged Elastic Band + --=================================================================== + if self.niter > self._climbing and self:climbing(image) then + local F = self[image].F + NEB_F = F - 2 * F:project( self:tangent(image) ) + else + DNEB_F = 0.0 + NEB_F = self:perpendicular_force(image) + self:spring_force(image) + DNEB_F + end + return NEB_F + end +--- Query the current force (same as `NEB:force` but with IO included) +-- @int image the image +-- @return force +function VCNEB:force(image, IO) + self:_check_image(image) + if image == 1 then + -- Increment step-counter + self.niter = self.niter + 1 + end + local F = self[image].F + local tangent = self:tangent(image) + local perp_F = self:perpendicular_force(image) + local spring_F = self:spring_force(image) + local NEB_F = self:neb_force(image) + -- Things I want to output in files as control (all in 3xN format) + if IO then + local f + -- Current coordinates (ie .R) + f = io.open( ("VCNEB.%d.R"):format(image), "a") + self[image].R:savetxt(f) + f:close() + -- Forces before (ie .F) + f = io.open( ("VCNEB.%d.F"):format(image), "a") + F:savetxt(f) + f:close() + -- Perpendicular force + f = io.open( ("VCNEB.%d.F.P"):format(image), "a") + perp_F:savetxt(f) + f:close() + -- Spring force + f = io.open( ("VCNEB.%d.F.S"):format(image), "a") + spring_F:savetxt(f) + f:close() + -- NEB Force + f = io.open( ("VCNEB.%d.F.NEB"):format(image), "a") + NEB_F:savetxt(f) + f:close() + -- Tangent + f = io.open( ("VCNEB.%d.T"):format(image), "a") + tangent:savetxt(f) + f:close() + -- dR - previous reaction coordinate + f = io.open( ("VCNEB.%d.dR_prev"):format(image), "a") + self:dR(image-1, image):savetxt(f) + f:close() + -- dR - next reaction coordinate + f = io.open( ("VCNEB.%d.dR_next"):format(image), "a") + self:dR(image, image+1):savetxt(f) + f:close() + end + -- Fake return to test + return NEB_F +end +--- Store the current step of the NEB iteration with the appropriate results +function VCNEB:save(IO) + -- If we should not do IO, return immediately + if not IO then + return + end + -- local E0 + local E0 = self[0].E + -- Now setup the matrix to write the NEB-results + local dat = array.Array( self.n_images + 2, 6) + for i = 0, self.n_images + 1 do + local row = dat[i+1] + -- image number (0 for initial, n_images + 1 for final) + row[1] = i + -- Accumulated reaction coordinate + if i == 0 then + row[2] = 0. + else + row[2] = dat[i][2] + self:dR(i-1, i):norm(0) + end + -- Total energy of current iteration + row[3] = self[i].E + -- Energy difference from initial image + row[4] = self[i].E - E0 + -- Image curvature + if i == 0 or i == self.n_images + 1 then + row[5] = 0. + else + row[5] = self:curvature(i) + end + -- Vector-norm of maximum force of the NEB-force + if i == 0 or i == self.n_images + 1 then + row[6] = 0. + else + row[6] = self:neb_force(i):norm():max() + end + end + local f = io.open("VCNEB.results", "a") + dat:savetxt(f) + f:close() +end + +--- Initialize all files that will be written to +function VCNEB:init_files() + -- We clean all image data for a new run + local function new_file(fname, ...) + local f = io.open(fname, 'w') + local a = {...} + for _, v in pairs(a) do + f:write("# " .. v .. "\n") + end + f:close() + end + new_file("VCNEB.results", "NEB results file", + "Image reaction-coordinate Energy E-diff Curvature F-max(atom)") + for img = 1, self.n_images do + new_file( ("VCNEB.%d.R"):format(img), "Coordinates") + new_file( ("VCNEB.%d.F"):format(img), "Constrained force") + new_file( ("VCNEB.%d.F.P"):format(img), "Perpendicular force") + new_file( ("VCNEB.%d.F.S"):format(img), "Spring force") + new_file( ("VCNEB.%d.F.NEB"):format(img), "Resulting NEB force") + new_file( ("VCNEB.%d.T"):format(img), "NEB tangent") + new_file( ("VCNEB.%d.dR_prev"):format(img), "Reaction distance (previous)") + new_file( ("VCNEB.%d.dR_next"):format(img), "Reaction distance (next)") + end +end +--- Print to screen some information regarding the NEB algorithm +function VCNEB:info() + print ("============================================") + print (" The Variable Cell NEB (VC-NEB) method ") + print ("============================================") + + print("VCNEB Number of Images : " .. self.n_images) + print("VCNEB Use Climbing After : " .. self._climbing .. " Steps") + local tmp = array.Array( self.n_images + 1 ) + tmp[1] = self:dR(0, 1):norm(0) + for i = 2, self.n_images + 1 do + tmp[i] = tmp[i-1] + self:dR(i-1, i):norm(0) + end + print("VCNEB Reaction Coordinates: ") + print(tostring(tmp)) + local tmp = array.Array( self.n_images ) + for i = 1, self.n_images do + tmp[i] = self.k[i] + end + print("VCNEB Spring Constant: ") + print(tostring(tmp)) +end +-- Calculatin Perpendicular Spring force +function VCNEB:perpendicular_spring_force(image) + self:_check_image(image) + if self:tangent(image):norm(0)==0.0 then + return self:spring_force(image) + else + local PS=self:spring_force(image):project(self:tangent(image)) + return self:spring_force(image)-PS + end +end +function VCNEB:file_exists(name)--name + --local name + --DM_name=tostring(name) + DM_name=name + --print ("DM_name is :" .. DM_name) + local check + --local DM_name = name + local f = io.open(DM_name, "r") --name + if f ~= nil then + io.close(f) + --check=true + --print("TRUE: The file ".. DM_name.. " Exist!") + return true + else + --print("False: The file ".. DM_name.. " Doesn't Exist!") + return false + --check=false + end + --return check +end + +return VCNEB diff --git a/tutorials/dneb/H.psf b/tutorials/dneb/H.psf new file mode 100644 index 0000000..25a223e --- /dev/null +++ b/tutorials/dneb/H.psf @@ -0,0 +1,1527 @@ + H ca nrl nc + ATM3 19-FEB-98 Troullier-Martins + 1s 1.00 r= 1.25/2p 0.00 r= 1.25/3d 0.00 r= 1.25/4f 0.00 r= 1.25/ + 4 0 863 0.247875217667E-02 0.125000000000E-01 1.00000000000 + Radial grid follows + 0.311788641354E-04 0.627499101025E-04 0.947180709413E-04 0.127088341742E-03 + 0.159865780426E-03 0.193055508533E-03 0.226662712027E-03 0.260692642102E-03 + 0.295150616003E-03 0.330042017859E-03 0.365372299523E-03 0.401146981422E-03 + 0.437371653424E-03 0.474051975707E-03 0.511193679647E-03 0.548802568709E-03 + 0.586884519361E-03 0.625445481983E-03 0.664491481805E-03 0.704028619843E-03 + 0.744063073857E-03 0.784601099310E-03 0.825649030352E-03 0.867213280805E-03 + 0.909300345168E-03 0.951916799631E-03 0.995069303102E-03 0.103876459825E-02 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Total number of images (excluding initial[0] and final[n_images+1]) +local n_images = 5 +local k_spring = 1 +--================================================================= +-- Load the FLOS module +local flos = require "flos" +-- The prefix of the files that contain the images +-- Table of image geometries +local images = {} + +-- The default output label of the DM files +-- Function for reading a geometry +local read_geom = function(filename) + local file = io.open(filename, "r") + local na = tonumber(file:read()) + local R = flos.Array.zeros(na, 3) + file:read() + local i = 0 + local function tovector(s) + local t = {} + s:gsub('%S+', function(n) t[#t+1] = tonumber(n) end) + return t + end + for i = 1, na do + local line = file:read() + if line == nil then break end + -- Get stuff into the R + local v = tovector(line) + R[i][1] = v[1] + R[i][2] = v[2] + R[i][3] = v[3] + end + file:close() + return R +end + +-- Now read in the images +for i = 0, n_images + 1 do + images[#images+1] = flos.MDStep{R=read_geom(image_label .. i .. ".xyz")} +end + +-- Now we have all images... +local NEB = flos.DNEB(images,{k=k_spring}) +if siesta.IONode then + NEB:info() +end +-- Remove global (we use NEB.n_images) +n_images = nil + +-- Setup each image relaxation method (note it is prepared for several +-- relaxation methods per-image) +local relax = {} +for i = 1, NEB.n_images do + -- Select the relaxation method + relax[i] = {} + relax[i][1] = flos.CG{beta='PR',restart='Powell', line=flos.Line{optimizer = flos.LBFGS{H0 = 1. / 25.} } } + -- add more relaxation schemes if needed ;) + --relax[i][2] = flos.CG{beta='PR',restart='Powell', line=flos.Line{optimizer = flos.LBFGS{H0 = 1. / 50.} } } + --relax[i][3] = flos.CG{beta='PR',restart='Powell', line=flos.Line{optimizer = flos.LBFGS{H0 = 1. / 75.} } } + --relax[i][4] = flos.LBFGS{H0 = 1. / 50} + --relax[i][5] = flos.FIRE{dt_init = 1., direction="global", correct="global"} + if siesta.IONode then + NEB:info() + end + +end + +-- Counter for controlling which image we are currently relaxing +local current_image = 1 + +-- Grab the unit table of siesta (it is already created +-- by SIESTA) +local Unit = siesta.Units + + +function siesta_comm() + + -- This routine does exchange of data with SIESTA + local ret_tbl = {} + + -- Do the actual communication with SIESTA + if siesta.state == siesta.INITIALIZE then + + -- In the initialization step we request the + -- convergence criteria + -- MD.MaxDispl + -- MD.MaxForceTol + siesta.receive({"Label", + "geom.xa", + "MD.MaxDispl", + "MD.MaxForceTol"}) + + -- Store the Label + label = tostring(siesta.Label) + + -- Print information + IOprint("\nLUA NEB calculator") + + -- Ensure we update the convergence criteria + -- from SIESTA (in this way one can ensure siesta options) + for img = 1, NEB.n_images do + IOprint(("\nLUA NEB relaxation method for image %d:"):format(img)) + for i = 1, #relax[img] do + relax[img][i].tolerance = siesta.MD.MaxForceTol * Unit.Ang / Unit.eV + relax[img][i].max_dF = siesta.MD.MaxDispl / Unit.Ang + + -- Print information for this relaxation method + if siesta.IONode then + relax[img][i]:info() + end + end + end + + -- This is only reached one time, and that it as the beginning... + -- be sure to set the corresponding values + siesta.geom.xa = NEB.initial.R * Unit.Ang + + IOprint("\nLUA/NEB initial state\n") + -- force the initial image to be the first one to run + current_image = 0 + siesta_update_DM(0, current_image) + --Write xyz File + siesta_update_xyz(current_image) + IOprint(NEB[current_image].R) + + ret_tbl = {'geom.xa'} + + end + + if siesta.state == siesta.MOVE then + + -- Here we are doing the actual LBFGS algorithm. + -- We retrieve the current coordinates, the forces + -- and whether the geometry has relaxed + siesta.receive({"geom.fa", + "E.total", + "MD.Relaxed"}) + + -- Store the old image that has been tested, + -- in this way we can check whether we have moved to + -- a new image. + local old_image = current_image + + ret_tbl = siesta_move(siesta) + + -- we need to re-organize the DM files for faster convergence + -- pass whether the image is the same + siesta_update_DM(old_image, current_image) + siesta_update_xyz(current_image) + IOprint(NEB[current_image].R) + + end + + siesta.send(ret_tbl) +end + +function siesta_move(siesta) + + -- Retrieve the atomic coordinates, forces and the energy + local fa = flos.Array.from(siesta.geom.fa) * Unit.Ang / Unit.eV + local E = siesta.E.total / Unit.eV + + -- First update the coordinates, forces and energy for the + -- just calculated image + NEB[current_image]:set{F=fa, E=E} + + if current_image == 0 then + -- Perform the final image, to retain that information + current_image = NEB.n_images + 1 + + -- Set the atomic coordinates for the final image + siesta.geom.xa = NEB[current_image].R * Unit.Ang + + IOprint("\nLUA/NEB final state\n") + --siesta_update_DM(0, current_image) + -- The siesta relaxation is already not set + return {'geom.xa'} + + elseif current_image == NEB.n_images + 1 then + + -- Start the NEB calculation + current_image = 1 + + -- Set the atomic coordinates for the final image + siesta.geom.xa = NEB[current_image].R * Unit.Ang + + IOprint(("\nLUA/NEB running NEB image %d / %d\n"):format(current_image, NEB.n_images)) + + -- The siesta relaxation is already not set + return {'geom.xa'} + + elseif current_image < NEB.n_images then + + current_image = current_image + 1 + + -- Set the atomic coordinates for the image + siesta.geom.xa = NEB[current_image].R * Unit.Ang + + IOprint(("\nLUA/NEB running NEB image %d / %d\n"):format(current_image, NEB.n_images)) + + -- The siesta relaxation is already not set + return {'geom.xa'} + + end + + -- First we figure out how perform the NEB optimizations + -- Now we have calculated all the systems and are ready for doing + -- an NEB MD step + + -- Global variable to check for the NEB convergence + -- Initially assume it has relaxed + local relaxed = true + + IOprint("\nNEB step") + local out_R = {} + + -- loop on all images and pass the updated forces to the mixing algorithm + for img = 1, NEB.n_images do + + -- Get the correct NEB force (note that the relaxation + -- methods require the negative force) + local F = NEB:force(img, siesta.IONode) + IOprint("NEB: max F on image ".. img .. + (" = %10.5f, climbing = %s"):format(F:norm():max(), + tostring(NEB:climbing(img))) ) + + -- Prepare the relaxation for image `img` + local all_xa, weight = {}, flos.Array( #relax[img] ) + for i = 1, #relax[img] do + all_xa[i] = relax[img][i]:optimize(NEB[img].R, F) + weight[i] = relax[img][i].weight + end + weight = weight / weight:sum() + + if #relax[img] > 1 then + IOprint("\n weighted average for relaxation: ", tostring(weight)) + end + + -- Calculate the new coordinates and figure out + -- if the algorithm has converged (all forces below) + local out_xa = all_xa[1] * weight[1] + relaxed = relaxed and relax[img][1]:optimized() + for i = 2, #relax[img] do + out_xa = out_xa + all_xa[i] * weight[i] + relaxed = relaxed and relax[img][i]:optimized() + end + + -- Copy the optimized coordinates to a table + out_R[img] = out_xa + + end + + -- Before we update the coordinates we will write + -- the current steps results to the result file + -- (this HAS to be done before updating the coordinates) + NEB:save( siesta.IONode ) + + -- Now we may copy over the coordinates (otherwise + -- we do a consecutive update, and then overwrite) + for img = 1, NEB.n_images do + NEB[img]:set{R=out_R[img]} + end + + -- Start over in case the system has not relaxed + current_image = 1 + if relaxed then + -- the final coordinates are returned + siesta.geom.xa = NEB.final.R * Unit.Ang + IOprint("\nLUA/NEB complete\n") + else + siesta.geom.xa = NEB[1].R * Unit.Ang + IOprint(("\nLUA/NEB running NEB image %d / %d\n"):format(current_image, NEB.n_images)) + end + + siesta.MD.Relaxed = relaxed + + return {"geom.xa", + "MD.Relaxed"} +end + +-- Function for retaining the DM files for the images so that we +-- can easily restart etc. +function siesta_update_DM(old, current) + + if not siesta.IONode then + -- only allow the IOnode to perform stuff... + return + end + -- Move about files so that we re-use old DM files + local DM = label .. ".DM" + local old_DM = DM .. "." .. tostring(old) + local current_DM = DM .. "." .. tostring(current) + local initial_DM = DM .. ".0" + local final_DM = DM .. ".".. tostring(NEB.n_images+1) + print ("The Label of Old DM is : " .. old_DM) + print ("The Label of Current DM is : " .. current_DM) + -- Saving initial DM + if old==0 and current==0 then + print("Removing DM for Resuming") + IOprint("Deleting " .. DM .. " for a clean restart...") + os.execute("rm " .. DM) + end + + if 0 <= old and old <= NEB.n_images+1 and NEB:file_exists(DM) then + -- store the current DM for restart purposes + IOprint("Saving " .. DM .. " to " .. old_DM) + os.execute("mv " .. DM .. " " .. old_DM) + elseif NEB:file_exists(DM) then + IOprint("Deleting " .. DM .. " for a clean restart...") + os.execute("rm " .. DM) + end + + if NEB:file_exists(current_DM) then + IOprint("Deleting " .. DM .. " for a clean restart...") + os.execute("rm " .. DM) + IOprint("Restoring " .. current_DM .. " to " .. DM) + os.execute("cp " .. current_DM .. " " .. DM) + end + +end + +function siesta_update_xyz(current) + if not siesta.IONode then + -- only allow the IOnode to perform stuff... + return + end + local xyz_label = image_label ..tostring(current)..".xyz" + --self:_n_images=self.n_images + --self:_check_image(image) + + local f=io.open(xyz_label,"w") + f:write(tostring(#NEB[current].R).."\n \n") + --f:write(tostring(initialize:self.n_images).."\n \n") + for i=1,#NEB[current].R do + f:write(string.format(" %19.17f",tostring(NEB[current].R[i][1])).. " "..string.format("%19.17f",tostring(NEB[current].R[i][2]))..string.format(" %19.17f",tostring(NEB[current].R[i][3])).."\n") + end + f:close() + -- +end diff --git a/tutorials/dneb/image_0.xyz b/tutorials/dneb/image_0.xyz new file mode 100644 index 0000000..401884b --- /dev/null +++ b/tutorials/dneb/image_0.xyz @@ -0,0 +1,8 @@ +6 + + 0.00000000000000000 0.00000000000000000 0.00000000000000000 + 0.75700000000000001 0.58599999999999997 0.00000000000000000 + -0.75700000000000001 0.58599999999999997 0.00000000000000000 + 0.00000000000000000 3.50000000000000000 0.00000000000000000 + 0.75700000000000001 2.91400000000000015 0.00000000000000000 + -0.75700000000000001 2.91400000000000015 0.00000000000000000 diff --git a/tutorials/dneb/image_1.xyz b/tutorials/dneb/image_1.xyz new file mode 100644 index 0000000..1210b4d --- /dev/null +++ b/tutorials/dneb/image_1.xyz @@ -0,0 +1,8 @@ +6 + + 0.00000000000000000 0.00000000000000000 0.00000000000000000 + 0.75700000000000001 0.58599999999999997 0.00000000000000000 + -0.75700000000000001 0.58599999999999997 0.00000000000000000 + 0.00000000000000000 3.50000000000000000 0.00000000000000000 + 0.96490412410712001 3.37813099239540016 -0.00000000001081656 + -0.37744952914238999 2.60290563485239979 -0.00000000003442383 diff --git a/tutorials/dneb/image_2.xyz b/tutorials/dneb/image_2.xyz new file mode 100644 index 0000000..47a8cc9 --- /dev/null +++ b/tutorials/dneb/image_2.xyz @@ -0,0 +1,8 @@ +6 + + 0.00000000000000000 0.00000000000000000 0.00000000000000000 + 0.75700000000000001 0.58599999999999997 0.00000000000000000 + -0.75700000000000001 0.58599999999999997 0.00000000000000000 + 0.00000000000000000 3.50000000000000000 0.00000000000000000 + 0.89310423714778997 3.88172627936399994 0.00000000006022632 + 0.11856375202357000 2.53428462767679985 -0.00000000002263071 diff --git a/tutorials/dneb/image_3.xyz b/tutorials/dneb/image_3.xyz new file mode 100644 index 0000000..0fdfed1 --- /dev/null +++ b/tutorials/dneb/image_3.xyz @@ -0,0 +1,8 @@ +6 + + 0.00000000000000000 0.00000000000000000 0.00000000000000000 + 0.75700000000000001 0.58599999999999997 0.00000000000000000 + -0.75700000000000001 0.58599999999999997 0.00000000000000000 + 0.00000000000000000 3.50000000000000000 0.00000000000000000 + 0.58055559869398998 4.27789569807150016 -0.00000000013800293 + 0.58550477911720999 2.72411190182240004 -0.00000000000684885 diff --git a/tutorials/dneb/image_4.xyz b/tutorials/dneb/image_4.xyz new file mode 100644 index 0000000..9a7faad --- /dev/null +++ b/tutorials/dneb/image_4.xyz @@ -0,0 +1,8 @@ +6 + + 0.00000000000000000 0.00000000000000000 0.00000000000000000 + 0.75700000000000001 0.58599999999999997 0.00000000000000000 + -0.75700000000000001 0.58599999999999997 0.00000000000000000 + 0.00000000000000000 3.50000000000000000 0.00000000000000000 + 0.12333019881412000 4.46322373409009998 -0.00000000000017072 + 0.89345325818734000 3.12075405874769984 -0.00000000000109440 diff --git a/tutorials/dneb/image_5.xyz b/tutorials/dneb/image_5.xyz new file mode 100644 index 0000000..31b8828 --- /dev/null +++ b/tutorials/dneb/image_5.xyz @@ -0,0 +1,8 @@ +6 + + 0.00000000000000000 0.00000000000000000 0.00000000000000000 + 0.75700000000000001 0.58599999999999997 0.00000000000000000 + -0.75700000000000001 0.58599999999999997 0.00000000000000000 + 0.00000000000000000 3.50000000000000000 0.00000000000000000 + -0.37575528316467999 4.39474329826770038 -0.00000000000054162 + 0.96434371202832003 3.61500329263990006 -0.00000000000051287 diff --git a/tutorials/dneb/image_6.xyz b/tutorials/dneb/image_6.xyz new file mode 100644 index 0000000..3324606 --- /dev/null +++ b/tutorials/dneb/image_6.xyz @@ -0,0 +1,8 @@ +6 + + 0.00000000000000000 0.00000000000000000 0.00000000000000000 + 0.75700000000000001 0.58599999999999997 0.00000000000000000 + -0.75700000000000001 0.58599999999999997 0.00000000000000000 + 0.00000000000000000 3.50000000000000000 0.00000000000000000 + -0.75700000000000001 4.08600000000000030 0.00000000000000000 + 0.75700000000000001 4.08600000000000030 0.00000000000000000 diff --git a/tutorials/dneb/input.fdf b/tutorials/dneb/input.fdf new file mode 100644 index 0000000..83f6c90 --- /dev/null +++ b/tutorials/dneb/input.fdf @@ -0,0 +1,44 @@ +SystemName Water molecule NEB (FLOS) +SystemLabel flos_h2o_neb +NumberOfAtoms 6 +NumberOfSpecies 2 + +# Settings required for Lua-NEB +# This is because Lua-NEB is not controlling +# which DM to re-use. +# These flags enables Lua to manage the DM files +DM.UseSaveDM true +DM.History.Depth 0 + +MinSCFIterations 3 +DM.MixingWeight 0.02 +MeshCutoff 250. Ry + +%block ChemicalSpeciesLabel + 1 8 O # Species index, atomic number, species label + 2 1 H +%endblock ChemicalSpeciesLabel + +LatticeConstant 1. Ang +%block LatticeVectors + 15. 0. 0. + 0. 15. 0. + 0. 0. 15. +%endblock + +AtomicCoordinatesFormat Ang +%block AtomicCoordinatesAndAtomicSpecies + 0.000 0.000 0.000 1 + 0.757 0.586 0.000 2 +-0.757 0.586 0.000 2 + 0.000 3.500 0.000 1 + 0.757 2.914 0.000 2 +-0.757 2.914 0.000 2 +%endblock AtomicCoordinatesAndAtomicSpecies + +%block Geometry.Constraints + atom [1 -- 4] +%endblock + +MD.TypeOfRun LUA +Lua.Script dneb_with_restart-new.lua diff --git a/tutorials/kpoint/H.psf b/tutorials/kpoint/H.psf new file mode 100644 index 0000000..25a223e --- /dev/null +++ b/tutorials/kpoint/H.psf @@ -0,0 +1,1527 @@ + H ca nrl nc + ATM3 19-FEB-98 Troullier-Martins + 1s 1.00 r= 1.25/2p 0.00 r= 1.25/3d 0.00 r= 1.25/4f 0.00 r= 1.25/ + 4 0 863 0.247875217667E-02 0.125000000000E-01 1.00000000000 + Radial grid follows + 0.311788641354E-04 0.627499101025E-04 0.947180709413E-04 0.127088341742E-03 + 0.159865780426E-03 0.193055508533E-03 0.226662712027E-03 0.260692642102E-03 + 0.295150616003E-03 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100644 index 0000000..d4dc767 --- /dev/null +++ b/tutorials/kpoint/input.fdf @@ -0,0 +1,32 @@ +SystemName Water molecule +SystemLabel test +NumberOfAtoms 3 +NumberOfSpecies 2 + +MeshCutoff 50. Ry + +%block ChemicalSpeciesLabel + 1 8 O # Species index, atomic number, species label + 2 1 H +%endblock ChemicalSpeciesLabel + +AtomicCoordinatesFormat Ang +%block AtomicCoordinatesAndAtomicSpecies + 0.000 0.000 0.000 1 + 0.757 0.586 0.000 2 +-0.757 0.586 0.000 2 +%endblock AtomicCoordinatesAndAtomicSpecies + +#MaxSCFIterations 5 +%block kgrid_Monkhorst_Pack + 5 0 0 0.0 + 0 5 0 0.0 + 0 0 1 0.0 +%endblock kgrid_Monkhorst_Pack + + +MD.TypeOfRun LUA + + + +Lua.Script kpoints.lua diff --git a/tutorials/kpoint/kpoints.lua b/tutorials/kpoint/kpoints.lua new file mode 100644 index 0000000..7fb91a5 --- /dev/null +++ b/tutorials/kpoint/kpoints.lua @@ -0,0 +1,246 @@ +--[[ +Example on how to converge the k-Mesh variable +in SIESTA. + +This example can take any system and will +perform a series of calculations with increasing +Mesh.Cutoff. +Finally it will write-out a table file to be plotted +which contains the k-Mesh vs Energy. + + - kgrid_Monkhorst_Pack + +This example may be controlled via total 9 values. for each direction we'll have : + + 1. kpoint_start_x + 2. kpoint_end_x + 3. kpoint_step_x + +where then this script will automatically create +an array of those values and iterate them. + +--]] + +local kpoint_start_x = 1. +local kpoint_end_x = 10. +local kpoint_step_x = 3. + +local kpoint_start_y = 1. +local kpoint_end_y = 10 +local kpoint_step_y = 3. + +local kpoint_start_z = 1. +local kpoint_end_z = 1. +local kpoint_step_z = 1. + +-- Load the FLOS module +local flos = require "flos" + +-- Create array for each kpoints cutoffs +local kpoint_cutoff_x = flos.Array.range(kpoint_start_x, kpoint_end_x, kpoint_step_x) +local kpoint_cutoff_y = flos.Array.range(kpoint_start_y, kpoint_end_y, kpoint_step_y) +local kpoint_cutoff_z = flos.Array.range(kpoint_start_z, kpoint_end_z, kpoint_step_z) + +local Total_kpoints = flos.Array.zeros(3) +Total_kpoints[1] = math.max(#kpoint_cutoff_x) +Total_kpoints[2] = math.max(#kpoint_cutoff_y) +Total_kpoints[3] = math.max(#kpoint_cutoff_z) +local kpoints_num = Total_kpoints:max() +local kpoint_mesh = flos.Array.zeros(9) +kpoint_mesh = kpoint_mesh:reshape(3,3) + +local Etot = flos.Array.zeros(kpoints_num) +-- Initial cut-off element +local ikpoint_x = 1 +local ikpoint_y = 1 +local ikpoint_z = 1 + +local kpoints_num_temp = 0 +function siesta_comm() + + -- Do the actual communication with SIESTA + if siesta.state == siesta.INITIALIZE then + + -- In the initialization step we request the + -- Mesh cutoff (merely to be able to set it + siesta.receive({"BZ.k.Matrix"}) + + -- Overwrite to ensure we start from the beginning + -- siesta.Mesh.Cutoff.Minimum = cutoff[icutoff] + -- siesta.kpoint_scf%k_cell + + kpoints = flos.Array.from(siesta.BZ.k.Matrix) + --cell_first = flos.Array.from(siesta.geom.cell) / Unit.Ang + + --IOprint( ("\nLUA: starting mesh-cutoff: %8.3f Ry\n"):format(cutoff[icutoff]) ) + -- IOprint(kpoint_scf%k_cell) + IOprint ("LUA: Provided k-point :" )--.. tostring( kpoints_num)) + + kpoint_mesh = kpoints + + IOprint("LUA: k_x :\n" .. tostring(kpoint_cutoff_x)) + IOprint("LUA: k_y :\n" .. tostring(kpoint_cutoff_y)) + IOprint("LUA: k_z :\n" .. tostring(kpoint_cutoff_z)) + + + --siesta.send({"Mesh.Cutoff.Minimum"}) + + IOprint("LUA: Total Number of k-points :" .. tostring(Total_kpoints:max() )) + + kpoint_mesh[1][1] = kpoint_start_x + kpoint_mesh[2][2] = kpoint_start_y + kpoint_mesh[3][3] = kpoint_start_y + + IOprint ("LUA: Number of k-points (".. tostring(kpoints_num_temp+1) .. "/" .. tostring(Total_kpoints:max()).. ")" ) + IOprint("LUA: Starting Kpoint :\n" .. tostring(kpoint_mesh)) + siesta.BZ.k.Matrix = kpoint_mesh + siesta.send({"BZ.k.Matrix"}) + end + + if siesta.state == siesta.INIT_MD then + + siesta.receive({"BZ.k.Matrix"}) + -- Store the used meshcutoff for this iteration + --cutoff[icutoff] = siesta.Mesh.Cutoff.Used + --IOprint(siesta.BZ.k.Matrix) + end + + if siesta.state == siesta.MOVE then + + -- Retrieve the total energy and update the + -- meshcutoff for the next cycle + -- Notice, we do not move, or change the geometry + -- or cell-vectors. + siesta.receive({"E.total", + "MD.Relaxed"}) + + Etot[ikpoint_x ] = siesta.E.total + + -- Step the meshcutoff for the next iteration + if step_kpointf_x(kpoint_cutoff_x[ikpoint_x]) then + kpoint_mesh[1][1] = kpoint_cutoff_x[ikpoint_x] + if step_kpointf_y(kpoint_cutoff_y[ikpoint_y]) then + kpoint_mesh[2][2] = kpoint_cutoff_y[ikpoint_y] + if step_kpointf_z(kpoint_cutoff_z[ikpoint_z]) then + kpoint_mesh[3][3] = kpoint_cutoff_z[ikpoint_z] + end + end + end + + --for i=1,3 do print(i) end + + --kpoint_mesh[1][1] = kpoint_cutoff_x[ikpoint_x] + -- kpoint_mesh[2][2] = kpoint_cutoff_y[ikpoint_y] + --kpoint_mesh[3][3] = kpoint_cutoff_z[ikpoint_z] + + --IOprint("Next Kpoint to Be Used : ".. tostring( ikpoint_x)) + --IOprint("kx :" .. tostring(kpoint_cutoff_x[ikpoint_x])) + --IOprint("ky :" .. tostring(kpoint_cutoff_y[ikpoint_y])) + --IOprint("kz :" .. tostring(kpoint_cutoff_z[ikpoint_z])) + + siesta.BZ.k.Matrix = kpoint_mesh + +-- IOprint (siesta.BZ.k.Matrix) + --IOprint(tostring(step_kpointf[ikpoint])) + --siesta.BZ.k.Matrix = kpoint[ikpoint] + --else + --end + --end + --end + kpoints_num_temp = kpoints_num_temp + 1 + --IOprint("Iterations : " .. tostring(kpoints_num_temp)) + + if kpoints_num == kpoints_num_temp then + siesta.MD.Relaxed = true + else + --IOprint("Next Kpoint to Be Used :\n") --.. tostring( ikpoint_x)) + --IOprint("kx :" .. tostring(kpoint_cutoff_x[ikpoint_x])) + --IOprint("ky :" .. tostring(kpoint_cutoff_y[ikpoint_y])) + --IOprint("kz :" .. tostring(kpoint_cutoff_z[ikpoint_z])) + --IOprint (siesta.BZ.k.Matrix) + --IOprint("Iterations : " .. tostring(kpoints_num_temp)) + IOprint ("LUA: Number of k-points (".. tostring(kpoints_num_temp+1) .. "/" .. tostring(Total_kpoints:max()).. ")" ) + IOprint("LUA: Next Kpoint to Be Used :\n" .. tostring(siesta.BZ.k.Matrix)) + end + + siesta.send({"BZ.k.Matrix", "MD.Relaxed"}) + + end + + if siesta.state == siesta.ANALYSIS then + local file = io.open("k_meshcutoff_E.dat", "w") + + file:write("# kpoint-Mesh-cutoff vs. energy\n") + + -- We write out a table with mesh-cutoff, the difference between + -- the last iteration, and the actual value + --file:write( ("%8.3e %17.10e %17.10e\n"):format(kpoint_cutoff_x[1], Etot[1], 0.) ) + file:write( ("%8.3e %17.10e %17.10e\n"):format(1, Etot[1], 0.) ) + + --for i = 2, #kpoint_cutoff_x do + for i = 2, Total_kpoints:max() do + --file:write( ("%8.3e %8.3e %8.3e %17.10e %17.10e\n"):format(kpoint_cutoff_x[i], + file:write( ("%8.3e %17.10e %17.10e\n"):format(i,Etot[i], Etot[i]-Etot[i-1]) ) + end + + file:close() + + end + +end + +-- Step the cutoff counter and return +-- true if successfull (i.e. if there are +-- any more to check left). +-- This function will also step past values +function step_kpointf_x(cur_kpoint_x) + + if ikpoint_x < #kpoint_cutoff_x then + ikpoint_x = ikpoint_x + 1 + else + return false + end + + if kpoint_cutoff_x[ikpoint_x] <= cur_kpoint_x then + kpoint_cutoff_x[ikpoint_x] = kpoint_cutoff_x[ikpoint_x-1] + Etot[ikpoint_x] = Etot[ikpoint_x-1] + return step_kpointf_x(cur_kpoint_x) + end + + return true +end + +function step_kpointf_y(cur_kpoint_y) + + if ikpoint_y < #kpoint_cutoff_y then + ikpoint_y = ikpoint_y + 1 + else + return false + end + + if kpoint_cutoff_y[ikpoint_y] <= cur_kpoint_y then + kpoint_cutoff_y[ikpoint_y] = kpoint_cutoff_y[ikpoint_y-1] + Etot[ikpoint_y] = Etot[ikpoint_y-1] + return step_kpointf_y(cur_kpoint_y) + end + + return true +end + +function step_kpointf_z(cur_kpoint_z) + + if ikpoint_z < #kpoint_cutoff_z then + ikpoint_z = ikpoint_z + 1 + else + return false + end + + if kpoint_cutoff_z[ikpoint_z] <= cur_kpoint_z then + kpoint_cutoff_z[ikpoint_z] = kpoint_cutoff_x[ikpoint_z-1] + Etot[ikpoint_z] = Etot[ikpoint_z-1] + return step_kpointf_z(cur_kpoint_z) + end + + return true +end + diff --git a/tutorials/mesh/H.psf b/tutorials/mesh/H.psf new file mode 100644 index 0000000..25a223e --- /dev/null +++ b/tutorials/mesh/H.psf @@ -0,0 +1,1527 @@ + H ca nrl nc + ATM3 19-FEB-98 Troullier-Martins + 1s 1.00 r= 1.25/2p 0.00 r= 1.25/3d 0.00 r= 1.25/4f 0.00 r= 1.25/ + 4 0 863 0.247875217667E-02 0.125000000000E-01 1.00000000000 + Radial grid follows + 0.311788641354E-04 0.627499101025E-04 0.947180709413E-04 0.127088341742E-03 + 0.159865780426E-03 0.193055508533E-03 0.226662712027E-03 0.260692642102E-03 + 0.295150616003E-03 0.330042017859E-03 0.365372299523E-03 0.401146981422E-03 + 0.437371653424E-03 0.474051975707E-03 0.511193679647E-03 0.548802568709E-03 + 0.586884519361E-03 0.625445481983E-03 0.664491481805E-03 0.704028619843E-03 + 0.744063073857E-03 0.784601099310E-03 0.825649030352E-03 0.867213280805E-03 + 0.909300345168E-03 0.951916799631E-03 0.995069303102E-03 0.103876459825E-02 + 0.108300951254E-02 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+Mesh.Cutoff. +Finally it will write-out a table file to be plotted +which contains the Mesh.Cutoff vs. + + - MeshCutoff + +This example may be controlled via 3 values: + + 1. cutoff_start + 2. cutoff_end + 3. cutoff_step + +where then this script will automatically create +an array of those values and iterate them. +Note the values here are in Ry. + +--]] + +local cutoff_start = 50. +local cutoff_end = 650. +local cutoff_step = 50. + +-- Load the FLOS module +local flos = require "flos" + +-- Create array of cut-offs +local cutoff = flos.Array.range(cutoff_start, cutoff_end, cutoff_step) +local Etot = flos.Array.zeros(#cutoff) +-- Initial cut-off element +local icutoff = 1 + +function siesta_comm() + + -- Do the actual communication with SIESTA + if siesta.state == siesta.INITIALIZE then + + -- In the initialization step we request the + -- Mesh cutoff (merely to be able to set it + siesta.receive({"Mesh.Cutoff.Minimum"}) + + -- Overwrite to ensure we start from the beginning + siesta.Mesh.Cutoff.Minimum = cutoff[icutoff] + + IOprint( ("\nLUA: starting mesh-cutoff: %8.3f Ry\n"):format(cutoff[icutoff]) ) + + siesta.send({"Mesh.Cutoff.Minimum"}) + + end + + if siesta.state == siesta.INIT_MD then + + siesta.receive({"Mesh.Cutoff.Used"}) + -- Store the used meshcutoff for this iteration + cutoff[icutoff] = siesta.Mesh.Cutoff.Used + + end + + if siesta.state == siesta.MOVE then + + -- Retrieve the total energy and update the + -- meshcutoff for the next cycle + -- Notice, we do not move, or change the geometry + -- or cell-vectors. + siesta.receive({"E.total", + "MD.Relaxed"}) + + Etot[icutoff] = siesta.E.total + + -- Step the meshcutoff for the next iteration + if step_cutoff(cutoff[icutoff]) then + siesta.Mesh.Cutoff.Minimum = cutoff[icutoff] + else + siesta.MD.Relaxed = true + end + + siesta.send({"Mesh.Cutoff.Minimum", "MD.Relaxed"}) + + end + + if siesta.state == siesta.ANALYSIS then + local file = io.open("meshcutoff_E.dat", "w") + + file:write("# Mesh-cutoff vs. energy\n") + + -- We write out a table with mesh-cutoff, the difference between + -- the last iteration, and the actual value + file:write( ("%8.3e %17.10e %17.10e\n"):format(cutoff[1], Etot[1], 0.) ) + for i = 2, #cutoff do + file:write( ("%8.3e %17.10e %17.10e\n"):format(cutoff[i], Etot[i], Etot[i]-Etot[i-1]) ) + end + + file:close() + + end + +end + +-- Step the cutoff counter and return +-- true if successfull (i.e. if there are +-- any more to check left). +-- This function will also step past values +function step_cutoff(cur_cutoff) + + if icutoff < #cutoff then + icutoff = icutoff + 1 + else + return false + end + + if cutoff[icutoff] <= cur_cutoff then + cutoff[icutoff] = cutoff[icutoff-1] + Etot[icutoff] = Etot[icutoff-1] + return step_cutoff(cur_cutoff) + end + + return true +end + diff --git a/tutorials/mesh/input.fdf b/tutorials/mesh/input.fdf new file mode 100644 index 0000000..c09886b --- /dev/null +++ b/tutorials/mesh/input.fdf @@ -0,0 +1,26 @@ +SystemName Water molecule +SystemLabel test +NumberOfAtoms 3 +NumberOfSpecies 2 + +MeshCutoff 50. Ry + +%block ChemicalSpeciesLabel + 1 8 O # Species index, atomic number, species label + 2 1 H +%endblock ChemicalSpeciesLabel + +AtomicCoordinatesFormat Ang +%block AtomicCoordinatesAndAtomicSpecies + 0.000 0.000 0.000 1 + 0.757 0.586 0.000 2 +-0.757 0.586 0.000 2 +%endblock AtomicCoordinatesAndAtomicSpecies + +#MaxSCFIterations 5 + +MD.TypeOfRun LUA + + + +Lua.Script conv_meshcutoff.lua diff --git a/tutorials/neb/H.psf b/tutorials/neb/H.psf new file mode 100644 index 0000000..25a223e --- /dev/null +++ b/tutorials/neb/H.psf @@ -0,0 +1,1527 @@ + H ca nrl nc + ATM3 19-FEB-98 Troullier-Martins + 1s 1.00 r= 1.25/2p 0.00 r= 1.25/3d 0.00 r= 1.25/4f 0.00 r= 1.25/ + 4 0 863 0.247875217667E-02 0.125000000000E-01 1.00000000000 + Radial grid follows + 0.311788641354E-04 0.627499101025E-04 0.947180709413E-04 0.127088341742E-03 + 0.159865780426E-03 0.193055508533E-03 0.226662712027E-03 0.260692642102E-03 + 0.295150616003E-03 0.330042017859E-03 0.365372299523E-03 0.401146981422E-03 + 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100644 index 0000000..401884b --- /dev/null +++ b/tutorials/neb/image_0.xyz @@ -0,0 +1,8 @@ +6 + + 0.00000000000000000 0.00000000000000000 0.00000000000000000 + 0.75700000000000001 0.58599999999999997 0.00000000000000000 + -0.75700000000000001 0.58599999999999997 0.00000000000000000 + 0.00000000000000000 3.50000000000000000 0.00000000000000000 + 0.75700000000000001 2.91400000000000015 0.00000000000000000 + -0.75700000000000001 2.91400000000000015 0.00000000000000000 diff --git a/tutorials/neb/image_1.xyz b/tutorials/neb/image_1.xyz new file mode 100644 index 0000000..6d0bed4 --- /dev/null +++ b/tutorials/neb/image_1.xyz @@ -0,0 +1,8 @@ +6 + + 0.00000000000000000 0.00000000000000000 0.00000000000000000 + 0.75700000000000001 0.58599999999999997 0.00000000000000000 + -0.75700000000000001 0.58599999999999997 0.00000000000000000 + 0.00000000000000000 3.50000000000000000 0.00000000000000000 + 0.96489652856039998 3.37813369419549980 0.00000000017816410 + -0.37744077752392002 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+ -0.75700000000000001 0.58599999999999997 0.00000000000000000 + 0.00000000000000000 3.50000000000000000 0.00000000000000000 + -0.37575528266087999 4.39474329760559979 0.00000000001522834 + 0.96434371199725999 3.61500329275569987 -0.00000000001371953 diff --git a/tutorials/neb/image_6.xyz b/tutorials/neb/image_6.xyz new file mode 100644 index 0000000..3324606 --- /dev/null +++ b/tutorials/neb/image_6.xyz @@ -0,0 +1,8 @@ +6 + + 0.00000000000000000 0.00000000000000000 0.00000000000000000 + 0.75700000000000001 0.58599999999999997 0.00000000000000000 + -0.75700000000000001 0.58599999999999997 0.00000000000000000 + 0.00000000000000000 3.50000000000000000 0.00000000000000000 + -0.75700000000000001 4.08600000000000030 0.00000000000000000 + 0.75700000000000001 4.08600000000000030 0.00000000000000000 diff --git a/tutorials/neb/input.fdf b/tutorials/neb/input.fdf new file mode 100644 index 0000000..905feb1 --- /dev/null +++ b/tutorials/neb/input.fdf @@ -0,0 +1,44 @@ +SystemName Water molecule NEB (FLOS) +SystemLabel flos_h2o_neb +NumberOfAtoms 6 +NumberOfSpecies 2 + +# Settings required for Lua-NEB +# This is because Lua-NEB is not controlling +# which DM to re-use. +# These flags enables Lua to manage the DM files +DM.UseSaveDM true +DM.History.Depth 0 + +MinSCFIterations 3 +DM.MixingWeight 0.02 +MeshCutoff 250. Ry + +%block ChemicalSpeciesLabel + 1 8 O # Species index, atomic number, species label + 2 1 H +%endblock ChemicalSpeciesLabel + +LatticeConstant 1. Ang +%block LatticeVectors + 15. 0. 0. + 0. 15. 0. + 0. 0. 15. +%endblock + +AtomicCoordinatesFormat Ang +%block AtomicCoordinatesAndAtomicSpecies + 0.000 0.000 0.000 1 + 0.757 0.586 0.000 2 +-0.757 0.586 0.000 2 + 0.000 3.500 0.000 1 + 0.757 2.914 0.000 2 +-0.757 2.914 0.000 2 +%endblock AtomicCoordinatesAndAtomicSpecies + +%block Geometry.Constraints + atom [1 -- 4] +%endblock + +MD.TypeOfRun LUA +Lua.Script neb_with_restart-new.lua diff --git a/tutorials/neb/neb_with_restart-new.lua b/tutorials/neb/neb_with_restart-new.lua new file mode 100644 index 0000000..f3e1376 --- /dev/null +++ b/tutorials/neb/neb_with_restart-new.lua @@ -0,0 +1,344 @@ +--[[ +Example on how to use an NEB method. +--]] +--================================================================= +local image_label = "image_" +-- Total number of images (excluding initial[0] and final[n_images+1]) +local n_images = 5 +local k_spring = 1 +--================================================================= +-- Load the FLOS module +local flos = require "flos" +-- The prefix of the files that contain the images +-- Table of image geometries +local images = {} + +-- The default output label of the DM files +-- Function for reading a geometry +local read_geom = function(filename) + local file = io.open(filename, "r") + local na = tonumber(file:read()) + local R = flos.Array.zeros(na, 3) + file:read() + local i = 0 + local function tovector(s) + local t = {} + s:gsub('%S+', function(n) t[#t+1] = tonumber(n) end) + return t + end + for i = 1, na do + local line = file:read() + if line == nil then break end + -- Get stuff into the R + local v = tovector(line) + R[i][1] = v[1] + R[i][2] = v[2] + R[i][3] = v[3] + end + file:close() + return R +end + +-- Now read in the images +for i = 0, n_images + 1 do + images[#images+1] = flos.MDStep{R=read_geom(image_label .. i .. ".xyz")} +end + +-- Now we have all images... +local NEB = flos.NEB(images,{k=k_spring}) +if siesta.IONode then + NEB:info() +end +-- Remove global (we use NEB.n_images) +n_images = nil + +-- Setup each image relaxation method (note it is prepared for several +-- relaxation methods per-image) +local relax = {} +for i = 1, NEB.n_images do + -- Select the relaxation method + relax[i] = {} + relax[i][1] = flos.CG{beta='PR',restart='Powell', line=flos.Line{optimizer = flos.LBFGS{H0 = 1. / 25.} } } + -- add more relaxation schemes if needed ;) + --relax[i][2] = flos.CG{beta='PR',restart='Powell', line=flos.Line{optimizer = flos.LBFGS{H0 = 1. / 50.} } } + --relax[i][3] = flos.CG{beta='PR',restart='Powell', line=flos.Line{optimizer = flos.LBFGS{H0 = 1. / 75.} } } + --relax[i][4] = flos.LBFGS{H0 = 1. / 50} + --relax[i][5] = flos.FIRE{dt_init = 1., direction="global", correct="global"} + if siesta.IONode then + NEB:info() + end + +end + +-- Counter for controlling which image we are currently relaxing +local current_image = 1 + +-- Grab the unit table of siesta (it is already created +-- by SIESTA) +local Unit = siesta.Units + + +function siesta_comm() + + -- This routine does exchange of data with SIESTA + local ret_tbl = {} + + -- Do the actual communication with SIESTA + if siesta.state == siesta.INITIALIZE then + + -- In the initialization step we request the + -- convergence criteria + -- MD.MaxDispl + -- MD.MaxForceTol + siesta.receive({"Label", + "geom.xa", + "MD.MaxDispl", + "MD.MaxForceTol"}) + + -- Store the Label + label = tostring(siesta.Label) + + -- Print information + IOprint("\nLUA NEB calculator") + + -- Ensure we update the convergence criteria + -- from SIESTA (in this way one can ensure siesta options) + for img = 1, NEB.n_images do + IOprint(("\nLUA NEB relaxation method for image %d:"):format(img)) + for i = 1, #relax[img] do + relax[img][i].tolerance = siesta.MD.MaxForceTol * Unit.Ang / Unit.eV + relax[img][i].max_dF = siesta.MD.MaxDispl / Unit.Ang + + -- Print information for this relaxation method + if siesta.IONode then + relax[img][i]:info() + end + end + end + + -- This is only reached one time, and that it as the beginning... + -- be sure to set the corresponding values + siesta.geom.xa = NEB.initial.R * Unit.Ang + + IOprint("\nLUA/NEB initial state\n") + -- force the initial image to be the first one to run + current_image = 0 + siesta_update_DM(0, current_image) + --Write xyz File + siesta_update_xyz(current_image) + IOprint(NEB[current_image].R) + + ret_tbl = {'geom.xa'} + + end + + if siesta.state == siesta.MOVE then + + -- Here we are doing the actual LBFGS algorithm. + -- We retrieve the current coordinates, the forces + -- and whether the geometry has relaxed + siesta.receive({"geom.fa", + "E.total", + "MD.Relaxed"}) + + -- Store the old image that has been tested, + -- in this way we can check whether we have moved to + -- a new image. + local old_image = current_image + + ret_tbl = siesta_move(siesta) + + -- we need to re-organize the DM files for faster convergence + -- pass whether the image is the same + siesta_update_DM(old_image, current_image) + siesta_update_xyz(current_image) + IOprint(NEB[current_image].R) + + end + + siesta.send(ret_tbl) +end + +function siesta_move(siesta) + + -- Retrieve the atomic coordinates, forces and the energy + local fa = flos.Array.from(siesta.geom.fa) * Unit.Ang / Unit.eV + local E = siesta.E.total / Unit.eV + + -- First update the coordinates, forces and energy for the + -- just calculated image + NEB[current_image]:set{F=fa, E=E} + + if current_image == 0 then + -- Perform the final image, to retain that information + current_image = NEB.n_images + 1 + + -- Set the atomic coordinates for the final image + siesta.geom.xa = NEB[current_image].R * Unit.Ang + + IOprint("\nLUA/NEB final state\n") + --siesta_update_DM(0, current_image) + -- The siesta relaxation is already not set + return {'geom.xa'} + + elseif current_image == NEB.n_images + 1 then + + -- Start the NEB calculation + current_image = 1 + + -- Set the atomic coordinates for the final image + siesta.geom.xa = NEB[current_image].R * Unit.Ang + + IOprint(("\nLUA/NEB running NEB image %d / %d\n"):format(current_image, NEB.n_images)) + + -- The siesta relaxation is already not set + return {'geom.xa'} + + elseif current_image < NEB.n_images then + + current_image = current_image + 1 + + -- Set the atomic coordinates for the image + siesta.geom.xa = NEB[current_image].R * Unit.Ang + + IOprint(("\nLUA/NEB running NEB image %d / %d\n"):format(current_image, NEB.n_images)) + + -- The siesta relaxation is already not set + return {'geom.xa'} + + end + + -- First we figure out how perform the NEB optimizations + -- Now we have calculated all the systems and are ready for doing + -- an NEB MD step + + -- Global variable to check for the NEB convergence + -- Initially assume it has relaxed + local relaxed = true + + IOprint("\nNEB step") + local out_R = {} + + -- loop on all images and pass the updated forces to the mixing algorithm + for img = 1, NEB.n_images do + + -- Get the correct NEB force (note that the relaxation + -- methods require the negative force) + local F = NEB:force(img, siesta.IONode) + IOprint("NEB: max F on image ".. img .. + (" = %10.5f, climbing = %s"):format(F:norm():max(), + tostring(NEB:climbing(img))) ) + + -- Prepare the relaxation for image `img` + local all_xa, weight = {}, flos.Array( #relax[img] ) + for i = 1, #relax[img] do + all_xa[i] = relax[img][i]:optimize(NEB[img].R, F) + weight[i] = relax[img][i].weight + end + weight = weight / weight:sum() + + if #relax[img] > 1 then + IOprint("\n weighted average for relaxation: ", tostring(weight)) + end + + -- Calculate the new coordinates and figure out + -- if the algorithm has converged (all forces below) + local out_xa = all_xa[1] * weight[1] + relaxed = relaxed and relax[img][1]:optimized() + for i = 2, #relax[img] do + out_xa = out_xa + all_xa[i] * weight[i] + relaxed = relaxed and relax[img][i]:optimized() + end + + -- Copy the optimized coordinates to a table + out_R[img] = out_xa + + end + + -- Before we update the coordinates we will write + -- the current steps results to the result file + -- (this HAS to be done before updating the coordinates) + NEB:save( siesta.IONode ) + + -- Now we may copy over the coordinates (otherwise + -- we do a consecutive update, and then overwrite) + for img = 1, NEB.n_images do + NEB[img]:set{R=out_R[img]} + end + + -- Start over in case the system has not relaxed + current_image = 1 + if relaxed then + -- the final coordinates are returned + siesta.geom.xa = NEB.final.R * Unit.Ang + IOprint("\nLUA/NEB complete\n") + else + siesta.geom.xa = NEB[1].R * Unit.Ang + IOprint(("\nLUA/NEB running NEB image %d / %d\n"):format(current_image, NEB.n_images)) + end + + siesta.MD.Relaxed = relaxed + + return {"geom.xa", + "MD.Relaxed"} +end + +-- Function for retaining the DM files for the images so that we +-- can easily restart etc. +function siesta_update_DM(old, current) + + if not siesta.IONode then + -- only allow the IOnode to perform stuff... + return + end + -- Move about files so that we re-use old DM files + local DM = label .. ".DM" + local old_DM = DM .. "." .. tostring(old) + local current_DM = DM .. "." .. tostring(current) + local initial_DM = DM .. ".0" + local final_DM = DM .. ".".. tostring(NEB.n_images+1) + print ("The Label of Old DM is : " .. old_DM) + print ("The Label of Current DM is : " .. current_DM) + -- Saving initial DM + if old==0 and current==0 then + print("Removing DM for Resuming") + IOprint("Deleting " .. DM .. " for a clean restart...") + os.execute("rm " .. DM) + end + + if 0 <= old and old <= NEB.n_images+1 and NEB:file_exists(DM) then + -- store the current DM for restart purposes + IOprint("Saving " .. DM .. " to " .. old_DM) + os.execute("mv " .. DM .. " " .. old_DM) + elseif NEB:file_exists(DM) then + IOprint("Deleting " .. DM .. " for a clean restart...") + os.execute("rm " .. DM) + end + + if NEB:file_exists(current_DM) then + IOprint("Deleting " .. DM .. " for a clean restart...") + os.execute("rm " .. DM) + IOprint("Restoring " .. current_DM .. " to " .. DM) + os.execute("cp " .. current_DM .. " " .. DM) + end + +end + +function siesta_update_xyz(current) + if not siesta.IONode then + -- only allow the IOnode to perform stuff... + return + end + local xyz_label = image_label ..tostring(current)..".xyz" + --self:_n_images=self.n_images + --self:_check_image(image) + + local f=io.open(xyz_label,"w") + f:write(tostring(#NEB[current].R).."\n \n") + --f:write(tostring(initialize:self.n_images).."\n \n") + for i=1,#NEB[current].R do + f:write(string.format(" %19.17f",tostring(NEB[current].R[i][1])).. " "..string.format("%19.17f",tostring(NEB[current].R[i][2]))..string.format(" %19.17f",tostring(NEB[current].R[i][3])).."\n") + end + f:close() + -- +end diff --git a/tutorials/tneb/H.psf b/tutorials/tneb/H.psf new file mode 100644 index 0000000..25a223e --- /dev/null +++ b/tutorials/tneb/H.psf @@ -0,0 +1,1527 @@ + H ca nrl nc + ATM3 19-FEB-98 Troullier-Martins + 1s 1.00 r= 1.25/2p 0.00 r= 1.25/3d 0.00 r= 1.25/4f 0.00 r= 1.25/ + 4 0 863 0.247875217667E-02 0.125000000000E-01 1.00000000000 + Radial grid follows + 0.311788641354E-04 0.627499101025E-04 0.947180709413E-04 0.127088341742E-03 + 0.159865780426E-03 0.193055508533E-03 0.226662712027E-03 0.260692642102E-03 + 0.295150616003E-03 0.330042017859E-03 0.365372299523E-03 0.401146981422E-03 + 0.437371653424E-03 0.474051975707E-03 0.511193679647E-03 0.548802568709E-03 + 0.586884519361E-03 0.625445481983E-03 0.664491481805E-03 0.704028619843E-03 + 0.744063073857E-03 0.784601099310E-03 0.825649030352E-03 0.867213280805E-03 + 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b/tutorials/tneb/image_2.xyz @@ -0,0 +1,8 @@ +6 + + 0.00000000000000000 0.00000000000000000 0.00000000000000000 + 0.75700000000000001 0.58599999999999997 0.00000000000000000 + -0.75700000000000001 0.58599999999999997 0.00000000000000000 + 0.00000000000000000 3.50000000000000000 0.00000000000000000 + 0.88599088999999998 3.86258122999999998 0.00000000000000000 + 0.12899089000000000 2.55141877000000017 0.00000000000000000 diff --git a/tutorials/tneb/image_3.xyz b/tutorials/tneb/image_3.xyz new file mode 100644 index 0000000..9b0c61e --- /dev/null +++ b/tutorials/tneb/image_3.xyz @@ -0,0 +1,8 @@ +6 + + 0.00000000000000000 0.00000000000000000 0.00000000000000000 + 0.75700000000000001 0.58599999999999997 0.00000000000000000 + -0.75700000000000001 0.58599999999999997 0.00000000000000000 + 0.00000000000000000 3.50000000000000000 0.00000000000000000 + 0.58599999999999997 4.25699999999999967 0.00000000000000000 + 0.58599999999999997 2.74299999999999988 0.00000000000000000 diff --git a/tutorials/tneb/image_4.xyz b/tutorials/tneb/image_4.xyz new file mode 100644 index 0000000..c8fda5f --- /dev/null +++ b/tutorials/tneb/image_4.xyz @@ -0,0 +1,8 @@ +6 + + 0.00000000000000000 0.00000000000000000 0.00000000000000000 + 0.75700000000000001 0.58599999999999997 0.00000000000000000 + -0.75700000000000001 0.58599999999999997 0.00000000000000000 + 0.00000000000000000 3.50000000000000000 0.00000000000000000 + 0.12899089000000000 4.44858123000000028 0.00000000000000000 + 0.88599088999999998 3.13741877000000002 0.00000000000000000 diff --git a/tutorials/tneb/image_5.xyz b/tutorials/tneb/image_5.xyz new file mode 100644 index 0000000..db9742c --- /dev/null +++ b/tutorials/tneb/image_5.xyz @@ -0,0 +1,8 @@ +6 + + 0.00000000000000000 0.00000000000000000 0.00000000000000000 + 0.75700000000000001 0.58599999999999997 0.00000000000000000 + -0.75700000000000001 0.58599999999999997 0.00000000000000000 + 0.00000000000000000 3.50000000000000000 0.00000000000000000 + -0.36258122999999998 4.38599089000000042 0.00000000000000000 + 0.94858123000000005 3.62899088999999986 0.00000000000000000 diff --git a/tutorials/tneb/image_6.xyz b/tutorials/tneb/image_6.xyz new file mode 100644 index 0000000..3324606 --- /dev/null +++ b/tutorials/tneb/image_6.xyz @@ -0,0 +1,8 @@ +6 + + 0.00000000000000000 0.00000000000000000 0.00000000000000000 + 0.75700000000000001 0.58599999999999997 0.00000000000000000 + -0.75700000000000001 0.58599999999999997 0.00000000000000000 + 0.00000000000000000 3.50000000000000000 0.00000000000000000 + -0.75700000000000001 4.08600000000000030 0.00000000000000000 + 0.75700000000000001 4.08600000000000030 0.00000000000000000 diff --git a/tutorials/tneb/input.fdf b/tutorials/tneb/input.fdf new file mode 100644 index 0000000..fee1e64 --- /dev/null +++ b/tutorials/tneb/input.fdf @@ -0,0 +1,44 @@ +SystemName Water molecule NEB (FLOS) +SystemLabel flos_h2o_neb +NumberOfAtoms 6 +NumberOfSpecies 2 + +# Settings required for Lua-NEB +# This is because Lua-NEB is not controlling +# which DM to re-use. +# These flags enables Lua to manage the DM files +DM.UseSaveDM true +DM.History.Depth 0 + +MinSCFIterations 3 +DM.MixingWeight 0.02 +MeshCutoff 250. Ry + +%block ChemicalSpeciesLabel + 1 8 O # Species index, atomic number, species label + 2 1 H +%endblock ChemicalSpeciesLabel + +LatticeConstant 1. Ang +%block LatticeVectors + 15. 0. 0. + 0. 15. 0. + 0. 0. 15. +%endblock + +AtomicCoordinatesFormat Ang +%block AtomicCoordinatesAndAtomicSpecies + 0.000 0.000 0.000 1 + 0.757 0.586 0.000 2 +-0.757 0.586 0.000 2 + 0.000 3.500 0.000 1 + 0.757 2.914 0.000 2 +-0.757 2.914 0.000 2 +%endblock AtomicCoordinatesAndAtomicSpecies + +%block Geometry.Constraints + atom [1 -- 4] +%endblock + +MD.TypeOfRun LUA +Lua.Script tneb_with_restart-new.lua diff --git a/tutorials/tneb/tneb_with_restart-new.lua b/tutorials/tneb/tneb_with_restart-new.lua new file mode 100644 index 0000000..3b0256a --- /dev/null +++ b/tutorials/tneb/tneb_with_restart-new.lua @@ -0,0 +1,344 @@ +--[[ +Example on how to use an NEB method. +--]] +--================================================================= +local image_label = "image_" +-- Total number of images (excluding initial[0] and final[n_images+1]) +local n_images = 5 +local k_spring = 1 +--================================================================= +-- Load the FLOS module +local flos = require "flos" +-- The prefix of the files that contain the images +-- Table of image geometries +local images = {} + +-- The default output label of the DM files +-- Function for reading a geometry +local read_geom = function(filename) + local file = io.open(filename, "r") + local na = tonumber(file:read()) + local R = flos.Array.zeros(na, 3) + file:read() + local i = 0 + local function tovector(s) + local t = {} + s:gsub('%S+', function(n) t[#t+1] = tonumber(n) end) + return t + end + for i = 1, na do + local line = file:read() + if line == nil then break end + -- Get stuff into the R + local v = tovector(line) + R[i][1] = v[1] + R[i][2] = v[2] + R[i][3] = v[3] + end + file:close() + return R +end + +-- Now read in the images +for i = 0, n_images + 1 do + images[#images+1] = flos.MDStep{R=read_geom(image_label .. i .. ".xyz")} +end + +-- Now we have all images... +local NEB = flos.TNEB(images,{k=k_spring,neb_temp=3000.}) +if siesta.IONode then + NEB:info() +end +-- Remove global (we use NEB.n_images) +n_images = nil + +-- Setup each image relaxation method (note it is prepared for several +-- relaxation methods per-image) +local relax = {} +for i = 1, NEB.n_images do + -- Select the relaxation method + relax[i] = {} + relax[i][1] = flos.CG{beta='PR',restart='Powell', line=flos.Line{optimizer = flos.LBFGS{H0 = 1. / 25.} } } + -- add more relaxation schemes if needed ;) + --relax[i][2] = flos.CG{beta='PR',restart='Powell', line=flos.Line{optimizer = flos.LBFGS{H0 = 1. / 50.} } } + --relax[i][3] = flos.CG{beta='PR',restart='Powell', line=flos.Line{optimizer = flos.LBFGS{H0 = 1. / 75.} } } + --relax[i][4] = flos.LBFGS{H0 = 1. / 50} + --relax[i][5] = flos.FIRE{dt_init = 1., direction="global", correct="global"} + if siesta.IONode then + NEB:info() + end + +end + +-- Counter for controlling which image we are currently relaxing +local current_image = 1 + +-- Grab the unit table of siesta (it is already created +-- by SIESTA) +local Unit = siesta.Units + + +function siesta_comm() + + -- This routine does exchange of data with SIESTA + local ret_tbl = {} + + -- Do the actual communication with SIESTA + if siesta.state == siesta.INITIALIZE then + + -- In the initialization step we request the + -- convergence criteria + -- MD.MaxDispl + -- MD.MaxForceTol + siesta.receive({"Label", + "geom.xa", + "MD.MaxDispl", + "MD.MaxForceTol"}) + + -- Store the Label + label = tostring(siesta.Label) + + -- Print information + IOprint("\nLUA NEB calculator") + + -- Ensure we update the convergence criteria + -- from SIESTA (in this way one can ensure siesta options) + for img = 1, NEB.n_images do + IOprint(("\nLUA NEB relaxation method for image %d:"):format(img)) + for i = 1, #relax[img] do + relax[img][i].tolerance = siesta.MD.MaxForceTol * Unit.Ang / Unit.eV + relax[img][i].max_dF = siesta.MD.MaxDispl / Unit.Ang + + -- Print information for this relaxation method + if siesta.IONode then + relax[img][i]:info() + end + end + end + + -- This is only reached one time, and that it as the beginning... + -- be sure to set the corresponding values + siesta.geom.xa = NEB.initial.R * Unit.Ang + + IOprint("\nLUA/NEB initial state\n") + -- force the initial image to be the first one to run + current_image = 0 + siesta_update_DM(0, current_image) + --Write xyz File + siesta_update_xyz(current_image) + IOprint(NEB[current_image].R) + + ret_tbl = {'geom.xa'} + + end + + if siesta.state == siesta.MOVE then + + -- Here we are doing the actual LBFGS algorithm. + -- We retrieve the current coordinates, the forces + -- and whether the geometry has relaxed + siesta.receive({"geom.fa", + "E.total", + "MD.Relaxed"}) + + -- Store the old image that has been tested, + -- in this way we can check whether we have moved to + -- a new image. + local old_image = current_image + + ret_tbl = siesta_move(siesta) + + -- we need to re-organize the DM files for faster convergence + -- pass whether the image is the same + siesta_update_DM(old_image, current_image) + siesta_update_xyz(current_image) + IOprint(NEB[current_image].R) + + end + + siesta.send(ret_tbl) +end + +function siesta_move(siesta) + + -- Retrieve the atomic coordinates, forces and the energy + local fa = flos.Array.from(siesta.geom.fa) * Unit.Ang / Unit.eV + local E = siesta.E.total / Unit.eV + + -- First update the coordinates, forces and energy for the + -- just calculated image + NEB[current_image]:set{F=fa, E=E} + + if current_image == 0 then + -- Perform the final image, to retain that information + current_image = NEB.n_images + 1 + + -- Set the atomic coordinates for the final image + siesta.geom.xa = NEB[current_image].R * Unit.Ang + + IOprint("\nLUA/NEB final state\n") + --siesta_update_DM(0, current_image) + -- The siesta relaxation is already not set + return {'geom.xa'} + + elseif current_image == NEB.n_images + 1 then + + -- Start the NEB calculation + current_image = 1 + + -- Set the atomic coordinates for the final image + siesta.geom.xa = NEB[current_image].R * Unit.Ang + + IOprint(("\nLUA/NEB running NEB image %d / %d\n"):format(current_image, NEB.n_images)) + + -- The siesta relaxation is already not set + return {'geom.xa'} + + elseif current_image < NEB.n_images then + + current_image = current_image + 1 + + -- Set the atomic coordinates for the image + siesta.geom.xa = NEB[current_image].R * Unit.Ang + + IOprint(("\nLUA/NEB running NEB image %d / %d\n"):format(current_image, NEB.n_images)) + + -- The siesta relaxation is already not set + return {'geom.xa'} + + end + + -- First we figure out how perform the NEB optimizations + -- Now we have calculated all the systems and are ready for doing + -- an NEB MD step + + -- Global variable to check for the NEB convergence + -- Initially assume it has relaxed + local relaxed = true + + IOprint("\nNEB step") + local out_R = {} + + -- loop on all images and pass the updated forces to the mixing algorithm + for img = 1, NEB.n_images do + + -- Get the correct NEB force (note that the relaxation + -- methods require the negative force) + local F = NEB:force(img, siesta.IONode) + IOprint("NEB: max F on image ".. img .. + (" = %10.5f, climbing = %s"):format(F:norm():max(), + tostring(NEB:climbing(img))) ) + + -- Prepare the relaxation for image `img` + local all_xa, weight = {}, flos.Array( #relax[img] ) + for i = 1, #relax[img] do + all_xa[i] = relax[img][i]:optimize(NEB[img].R, F) + weight[i] = relax[img][i].weight + end + weight = weight / weight:sum() + + if #relax[img] > 1 then + IOprint("\n weighted average for relaxation: ", tostring(weight)) + end + + -- Calculate the new coordinates and figure out + -- if the algorithm has converged (all forces below) + local out_xa = all_xa[1] * weight[1] + relaxed = relaxed and relax[img][1]:optimized() + for i = 2, #relax[img] do + out_xa = out_xa + all_xa[i] * weight[i] + relaxed = relaxed and relax[img][i]:optimized() + end + + -- Copy the optimized coordinates to a table + out_R[img] = out_xa + + end + + -- Before we update the coordinates we will write + -- the current steps results to the result file + -- (this HAS to be done before updating the coordinates) + NEB:save( siesta.IONode ) + + -- Now we may copy over the coordinates (otherwise + -- we do a consecutive update, and then overwrite) + for img = 1, NEB.n_images do + NEB[img]:set{R=out_R[img]} + end + + -- Start over in case the system has not relaxed + current_image = 1 + if relaxed then + -- the final coordinates are returned + siesta.geom.xa = NEB.final.R * Unit.Ang + IOprint("\nLUA/NEB complete\n") + else + siesta.geom.xa = NEB[1].R * Unit.Ang + IOprint(("\nLUA/NEB running NEB image %d / %d\n"):format(current_image, NEB.n_images)) + end + + siesta.MD.Relaxed = relaxed + + return {"geom.xa", + "MD.Relaxed"} +end + +-- Function for retaining the DM files for the images so that we +-- can easily restart etc. +function siesta_update_DM(old, current) + + if not siesta.IONode then + -- only allow the IOnode to perform stuff... + return + end + -- Move about files so that we re-use old DM files + local DM = label .. ".DM" + local old_DM = DM .. "." .. tostring(old) + local current_DM = DM .. "." .. tostring(current) + local initial_DM = DM .. ".0" + local final_DM = DM .. ".".. tostring(NEB.n_images+1) + print ("The Label of Old DM is : " .. old_DM) + print ("The Label of Current DM is : " .. current_DM) + -- Saving initial DM + if old==0 and current==0 then + print("Removing DM for Resuming") + IOprint("Deleting " .. DM .. " for a clean restart...") + os.execute("rm " .. DM) + end + + if 0 <= old and old <= NEB.n_images+1 and NEB:file_exists(DM) then + -- store the current DM for restart purposes + IOprint("Saving " .. DM .. " to " .. old_DM) + os.execute("mv " .. DM .. " " .. old_DM) + elseif NEB:file_exists(DM) then + IOprint("Deleting " .. DM .. " for a clean restart...") + os.execute("rm " .. DM) + end + + if NEB:file_exists(current_DM) then + IOprint("Deleting " .. DM .. " for a clean restart...") + os.execute("rm " .. DM) + IOprint("Restoring " .. current_DM .. " to " .. DM) + os.execute("cp " .. current_DM .. " " .. DM) + end + +end + +function siesta_update_xyz(current) + if not siesta.IONode then + -- only allow the IOnode to perform stuff... + return + end + local xyz_label = image_label ..tostring(current)..".xyz" + --self:_n_images=self.n_images + --self:_check_image(image) + + local f=io.open(xyz_label,"w") + f:write(tostring(#NEB[current].R).."\n \n") + --f:write(tostring(initialize:self.n_images).."\n \n") + for i=1,#NEB[current].R do + f:write(string.format(" %19.17f",tostring(NEB[current].R[i][1])).. " "..string.format("%19.17f",tostring(NEB[current].R[i][2]))..string.format(" %19.17f",tostring(NEB[current].R[i][3])).."\n") + end + f:close() + -- +end diff --git a/tutorials/vcneb/Mg.psf b/tutorials/vcneb/Mg.psf new file mode 100644 index 0000000..20c589d --- /dev/null +++ b/tutorials/vcneb/Mg.psf @@ -0,0 +1,1877 @@ + Mg pb nrl pcec + ATM3 21-AUG-17 Troullier-Martins + 3s 2.00 r= 2.59/3p 0.00 r= 2.76/3d 0.00 r= 1.90/4f 0.00 r= 1.90/ + 4 0 1061 0.206562681389E-03 0.125000000000E-01 2.00000000000 + Radial grid follows + 0.259823867795E-05 0.522915917521E-05 0.789317257845E-05 0.105906951452E-04 + 0.133221483688E-04 0.160879590444E-04 0.188885593356E-04 0.217243868418E-04 + 0.245958846669E-04 0.275035014883E-04 0.304476916269E-04 0.334289151185E-04 + 0.364476377853E-04 0.395043313089E-04 0.425994733039E-04 0.457335473925E-04 + 0.489070432801E-04 0.521204568319E-04 0.553742901504E-04 0.586690516536E-04 + 0.620052561547E-04 0.653834249425E-04 0.688040858626E-04 0.722677734004E-04 + 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a/tutorials/vcneb/image_coordinates_4.xyz b/tutorials/vcneb/image_coordinates_4.xyz new file mode 100644 index 0000000..dbda9c1 --- /dev/null +++ b/tutorials/vcneb/image_coordinates_4.xyz @@ -0,0 +1,4 @@ +2 + + 1.80726405979580007 0.99097916558691002 10.01356773881600049 + 0.67908357770318994 -0.28592878803616001 10.59032969655000045 diff --git a/tutorials/vcneb/image_coordinates_5.xyz b/tutorials/vcneb/image_coordinates_5.xyz new file mode 100644 index 0000000..2fa5412 --- /dev/null +++ b/tutorials/vcneb/image_coordinates_5.xyz @@ -0,0 +1,4 @@ +2 + + 1.77381019954749997 1.07513100234270009 10.30251786275800008 + 0.30242866470417001 -0.10832459190651000 10.30330797610199944 diff --git a/tutorials/vcneb/image_coordinates_6.xyz b/tutorials/vcneb/image_coordinates_6.xyz new file mode 100644 index 0000000..7f4ca2e --- /dev/null +++ b/tutorials/vcneb/image_coordinates_6.xyz @@ -0,0 +1,4 @@ +2 + + 1.41913399999999990 1.41913399999999990 10.30300000000000082 + 0.00000000000000000 0.00000000000000000 10.30300000000000082 diff --git a/tutorials/vcneb/image_vectors_0.xyz b/tutorials/vcneb/image_vectors_0.xyz new file mode 100644 index 0000000..89a9532 --- /dev/null +++ b/tutorials/vcneb/image_vectors_0.xyz @@ -0,0 +1,5 @@ +3 + + 1.68629000000000007 -2.92073999999999989 0.00000000000000000 + 1.68629000000000007 2.92073999999999989 0.00000000000000000 + 0.00000000000000000 0.00000000000000000 20.60600000000000165 diff --git a/tutorials/vcneb/image_vectors_1.xyz b/tutorials/vcneb/image_vectors_1.xyz new file mode 100644 index 0000000..6d46d21 --- /dev/null +++ b/tutorials/vcneb/image_vectors_1.xyz @@ -0,0 +1,5 @@ +3 + + 1.88858780646279989 -2.43526587542240014 0.00000000000000000 + 1.41294872336649990 2.90856628598320022 0.00000000000000000 + 0.00000000000000000 0.00000000000000000 20.60600000000000165 diff --git a/tutorials/vcneb/image_vectors_2.xyz b/tutorials/vcneb/image_vectors_2.xyz new file mode 100644 index 0000000..d1b4b7a --- /dev/null +++ b/tutorials/vcneb/image_vectors_2.xyz @@ -0,0 +1,5 @@ +3 + + 2.08152528962430017 -1.94820283954630002 0.00000000000000000 + 1.13029823967390008 2.89479886948970000 0.00000000000000000 + 0.00000000000000000 0.00000000000000000 20.60600000000000165 diff --git a/tutorials/vcneb/image_vectors_3.xyz b/tutorials/vcneb/image_vectors_3.xyz new file mode 100644 index 0000000..e4bf301 --- /dev/null +++ b/tutorials/vcneb/image_vectors_3.xyz @@ -0,0 +1,5 @@ +3 + + 2.27456425468129986 -1.46115212965970009 0.00000000000000000 + 0.84772367975532004 2.88104617457489987 0.00000000000000000 + 0.00000000000000000 0.00000000000000000 20.60600000000000165 diff --git a/tutorials/vcneb/image_vectors_4.xyz b/tutorials/vcneb/image_vectors_4.xyz new file mode 100644 index 0000000..7ff9261 --- /dev/null +++ b/tutorials/vcneb/image_vectors_4.xyz @@ -0,0 +1,5 @@ +3 + + 2.46760321973810015 -0.97410141977317999 0.00000000000000000 + 0.56514911983687999 2.86729347965989989 0.00000000000000000 + 0.00000000000000000 0.00000000000000000 20.60600000000000165 diff --git a/tutorials/vcneb/image_vectors_5.xyz b/tutorials/vcneb/image_vectors_5.xyz new file mode 100644 index 0000000..62237c2 --- /dev/null +++ b/tutorials/vcneb/image_vectors_5.xyz @@ -0,0 +1,5 @@ +3 + + 2.66062897781830010 -0.48705047747426000 0.00000000000000000 + 0.28257315726624999 2.85353942308370012 0.00000000000000000 + 0.00000000000000000 0.00000000000000000 20.60600000000000165 diff --git a/tutorials/vcneb/image_vectors_6.xyz b/tutorials/vcneb/image_vectors_6.xyz new file mode 100644 index 0000000..05132ac --- /dev/null +++ b/tutorials/vcneb/image_vectors_6.xyz @@ -0,0 +1,5 @@ +3 + + 2.83826799999999979 0.00000000000000000 0.00000000000000000 + 0.00000000000000000 2.83826799999999979 0.00000000000000000 + 0.00000000000000000 0.00000000000000000 20.60600000000000165 diff --git a/tutorials/vcneb/input.fdf b/tutorials/vcneb/input.fdf new file mode 100644 index 0000000..72d3c76 --- /dev/null +++ b/tutorials/vcneb/input.fdf @@ -0,0 +1,90 @@ +# Created by GDIS version 0.90.0 +SystemLabel MgO-3x3x1-2V + +#---------------------------------------------------------- +# Crystal flags +#---------------------------------------------------------- +NumberOfAtoms 2 + +NumberOfSpecies 2 + +%block ChemicalSpeciesLabel + 1 12 Mg + 2 8 O +# 3 -8 VO +%endblock ChemicalSpeciesLabel + +LatticeConstant 1.0 Ang +%block LatticeVectors + 1.68629 -2.92074 0.000 + 1.68629 2.92074 0.000 + 0.00000 0.00000 20.606 +%endblock LatticeVectors + +AtomicCoordinatesFormat Ang +%block AtomicCoordinatesAndAtomicSpecies + 1.6862899831371 0.9735799902642 10.303 1 1 Mg + 1.6862899831371 -0.9735799902642 10.303 2 1 O +%endblock AtomicCoordinatesAndAtomicSpecies +#---------------------------------------------------------- +# Basis flags +#---------------------------------------------------------- +%block PAO.BasisSizes +Mg DZP +%endblock PAO.BasisSizes +%block PAO.Basis +O 3 -0.4158308 + n=2 0 2 E 25.2217485 -0.7787941 + 4.1893036 -0.5955594 + 1.00000 1.00000 + n=2 1 2 E 13.2644853 -0.7950761 + 6.0475603 -0.6742187 + 1.00000 1.00000 + n=3 2 2 E 45.9587470 -0.7957318 + 3.2675257 0.0 + 1.00000 1.0 +%endblock PAO.Basis +%block kgrid_Monkhorst_Pack +5 0 0 0.0 +0 5 0 0.0 +0 0 1 0.0 +%endblock kgrid_Monkhorst_Pack +MeshCutoff 300 Ry +XC.functional GGA +XC.authors revPBE +SpinPolarized .true. +#---------------------------------------------------------- +# DM flags +#---------------------------------------------------------- +DM.MixingWeight 0.20 +DM.NumberPulay 4 +DM.UseSaveDM .true. +DM.Tolerance 1.0d-4 +DM.History.Depth 0 +MaxSCFIterations 500 +#---------------------------------------------------------- +# MD flags +#---------------------------------------------------------- +MD.MaxCGDispl 0.5 Bohr +MD.TypeOfRun LUA +MD.VariableCell .True. +#MD.NumCGsteps 200 +MD.MaxForceTol 0.04000 eV/Ang +#MD.UseSaveXV .true. +MD.MaxStressTol 0.5 GPa +#---------------------------------------------------------- +# Electronic flags +#---------------------------------------------------------- +ElectronicTemperature 5 K +#NumberOfEigenStates 800 +#UseNewDiagk .false. +#Diag.ParallelOverK .false. +#LongOutput .true. +#WriteMDHistory .true. +#WriteMDXmol .true. +#COOP.Write .true. +#WriteMullikenPop 3 +#WriteHirshfeldPop T +#WriteVoronoiPop T +Lua.Script vc-neb_with_restart.lua + diff --git a/tutorials/vcneb/vc-neb_with_restart.lua b/tutorials/vcneb/vc-neb_with_restart.lua new file mode 100644 index 0000000..f525d4a --- /dev/null +++ b/tutorials/vcneb/vc-neb_with_restart.lua @@ -0,0 +1,459 @@ +--[[ +Example on how to use an NEB method. +--]] +-- Load the FLOS module +local flos = require "flos" +-- The prefix of the files that contain the images +local image_label = "image_coordinates_" +local image_vector_label= "image_vectors_" +-- Total number of images (excluding initial[0] and final[n_images+1]) +local n_images = 5 +-- Table of image geometries +local images = {} +local images_vectors={} +-- The default output label of the DM files +local f_label_xyz = image_label -- "image_coordinates_" +local f_label_xyz_vec = image_vector_label --"image_vectors_" +-- Function for reading a geometry and vector +local read_geom = function(filename) + local file = io.open(filename, "r") + local na = tonumber(file:read()) + local R = flos.Array.zeros(na, 3) + file:read() + local i = 0 + local function tovector(s) + local t = {} + s:gsub('%S+', function(n) t[#t+1] = tonumber(n) end) + return t + end + for i = 1, na do + local line = file:read() + if line == nil then break end + -- Get stuff into the R + local v = tovector(line) + R[i][1] = v[1] + R[i][2] = v[2] + R[i][3] = v[3] + end + file:close() + return R +end +-- Now read in the images +for i = 0, n_images + 1 do + images[#images+1] = flos.MDStep{R=read_geom(image_label .. i .. ".xyz")} + images_vectors[#images_vectors+1]= flos.MDStep{R=read_geom(image_vector_label .. i .. ".xyz")} +end +-- Now we have all images... +local NEB = flos.VCNEB(images,{k=1.0}) +local VCNEB = flos.VCNEB(images_vectors,{k=1.0}) + +if siesta.IONode then + NEB:info() + VCNEB:info() +end +-- Remove global (we use NEB.n_images) +n_images = nil +-- Setup each image relaxation method (note it is prepared for several +-- relaxation methods per-image) +local relax = {} +local vcrelax= {} +for i=1, NEB.n_images do + relax[i]={} + vcrelax[i]={} + relax[i][1] = flos.CG{beta='PR', line=flos.Line{optimizer = flos.LBFGS{H0 = 1. / 25.} } } + vcrelax[i][1] = flos.CG{beta='PR', line=flos.Line{optimizer = flos.LBFGS{H0 = 1. / 25.} } } + if siesta.IONode then + NEB:info() + VCNEB:info() + end + --relax[i][2] = flos.LBFGS{H0 = 1. / 50} + --relax[i][1] = flos.FIRE{dt_init = 1., direction="global", correct="global"} + -- add more relaxation schemes if needed ;) +end +-- Counter for controlling which image we are currently relaxing +local current_image = 1 +-- Grab the unit table of siesta (it is already created +-- by SIESTA) +local Unit = siesta.Units +function siesta_comm() + -- This routine does exchange of data with SIESTA + local ret_tbl = {} + -- Do the actual communication with SIESTA + if siesta.state == siesta.INITIALIZE then + -- In the initialization step we request the + -- convergence criteria + -- MD.MaxDispl + -- MD.MaxForceTol + siesta.receive({"Label", + "geom.xa", + "MD.MaxDispl", + "MD.MaxForceTol", + "MD.MaxStressTol", + "geom.cell", + "geom.stress"}) + -- Store the Label + label = tostring(siesta.Label) + --stress=flos.Array.from(siesta.geom.stress)* Unit.Ang ^ 3 / Unit.eV + -- Print information + IOprint("\nLUA NEB calculator") + -- Ensure we update the convergence criteria + -- from SIESTA (in this way one can ensure siesta options) + for img = 1, NEB.n_images do + IOprint(("\nLUA NEB relaxation method for image %d:"):format(img)) + for i = 1, #relax[img] do + relax[img][i].tolerance = siesta.MD.MaxForceTol * Unit.Ang / Unit.eV + relax[img][i].max_dF = siesta.MD.MaxDispl / Unit.Ang + vcrelax[img][i].tolerance = siesta.MD.MaxStressTol * Unit.Ang ^ 3 / Unit.eV + vcrelax[img][i].max_dF = siesta.MD.MaxDispl / Unit.Ang + -- Print information for this relaxation method + if siesta.IONode then + relax[img][i]:info() + vcrelax[img][i]:info() + end + end + end + -- This is only reached one time, and that it as the beginning... + -- be sure to set the corresponding values + siesta.geom.xa = NEB.initial.R * Unit.Ang + siesta.geom.cell = VCNEB.initial.R * Unit.Ang + IOprint("\nLUA/NEB initial state\n") + -- force the initial image to be the first one to run + --IOprint(VCNEB.zeros) + current_image = 0 + siesta_update_DM(0, current_image) + --Write xyz File + siesta_update_xyz(current_image) + siesta_update_xyz_vec(current_image) + --IOprint("============================================") + IOprint("Lattice Vector for image : ".. current_image) + IOprint(VCNEB[current_image].R) + -- IOprint("============================================") + IOprint("Atomic Coordinates for image : ".. current_image) + IOprint(NEB[current_image].R) + -- IOprint("============================================") + ret_tbl = {'geom.xa',"geom.stress","geom.cell"} + end + if siesta.state == siesta.MOVE then + -- Here we are doing the actual LBFGS algorithm. + -- We retrieve the current coordinates, the forces + -- and whether the geometry has relaxed + siesta.receive({"geom.fa", + "E.total", + "MD.Relaxed", + "geom.cell", + "geom.stress"}) + -- Store the old image that has been tested, + -- in this way we can check whether we have moved to + -- a new image. + local old_image = current_image + ret_tbl = siesta_move(siesta) + -- we need to re-organize the DM files for faster convergence + -- pass whether the image is the same + --stress=flos.Array.from(siesta.geom.stress)* Unit.Ang ^ 3 / Unit.eV + siesta_update_DM(old_image, current_image) + siesta_update_xyz(current_image) + siesta_update_xyz_vec(current_image) + --IOprint(stress) + end + siesta.send(ret_tbl) +end +function siesta_move(siesta) + -- Retrieve the atomic coordinates, forces and the energy + local fa = flos.Array.from(siesta.geom.fa) * Unit.Ang / Unit.eV + local E = siesta.E.total / Unit.eV + -- First update the coordinates, forces and energy for the + -- just calculated image + --print(fa) + NEB[current_image]:set{F=fa, E=E} + --[[ Retrieve the vector coordinates, forces and the energy --]] + --local cell=flos.Array.from(siesta.geom.cell)/ Unit.Ang + --local vol=cell[1]:cross(cell[2]):dot(cell[3]) + local Vfa = (-flos.Array.from(siesta.geom.stress) * Unit.Ang ^ 3 / Unit.eV)--* vol + local VE = siesta.E.total / Unit.eV + -- First update the coordinates, forces and energy for the + -- just calculated image + --print(Vfa) + VCNEB[current_image]:set{F=Vfa,E=VE} + --VCNEB:force(current_image, siesta.IONode) + if current_image == 0 then + -- Perform the final image, to retain that information + current_image = NEB.n_images + 1 + -- Set the atomic coordinates for the final image + siesta.geom.xa = NEB[current_image].R * Unit.Ang + siesta.geom.cell = VCNEB[current_image].R * Unit.Ang + IOprint("\nLUA/NEB final state\n") + IOprint("Lattice Vectors for Final Image") + IOprint(VCNEB[current_image].R) + --IOprint("Stresss") + --IOprint(VCNEB[current_image].F) + --IOprint(stress) + -- The siesta relaxation is already not set + return {'geom.xa',"geom.stress","geom.cell"} + elseif current_image == NEB.n_images + 1 then + -- Start the NEB calculation + current_image = 1 + -- Set the atomic coordinates for the final image + siesta.geom.xa = NEB[current_image].R * Unit.Ang + siesta.geom.cell = VCNEB[current_image].R * Unit.Ang + IOprint(("\nLUA/NEB running NEB image %d / %d\n"):format(current_image, NEB.n_images)) + IOprint("Lattice Vectors") + IOprint(VCNEB[current_image].R) + IOprint("Stresss") + IOprint(VCNEB[current_image].F) + -- The siesta relaxation is already not set + return {'geom.xa',"geom.stress","geom.cell"} + elseif current_image < NEB.n_images then + current_image = current_image + 1 + -- Set the atomic coordinates for the image + siesta.geom.xa = NEB[current_image].R * Unit.Ang + siesta.geom.cell = VCNEB[current_image].R * Unit.Ang + IOprint(("\nLUA/NEB running NEB image %d / %d\n"):format(current_image, NEB.n_images)) + IOprint("Lattice Vectors") + IOprint(VCNEB[current_image].R) + IOprint("Stresss") + IOprint(VCNEB[current_image].F) + --IOprint(NEB.tangent) + -- The siesta relaxation is already not set + return {'geom.xa',"geom.stress","geom.cell"} + end + -- First we figure out how perform the NEB optimizations + -- Now we have calculated all the systems and are ready for doing + -- an NEB MD step + -- Global variable to check for the NEB convergence + -- Initially assume it has relaxed + local relaxed = true + local vcrelaxed = true + local tot_relax= false + IOprint("\nNEB step") + local out_R = {} + local out_VR = {} + -- loop on all images and pass the updated forces to the mixing algorithm + for img = 1, NEB.n_images do + -- Get the correct NEB force (note that the relaxation + -- methods require the negative force) + local F = NEB:force(img, siesta.IONode) + IOprint("NEB: max F on image ".. img .. + (" = %10.5f, climbing = %s"):format(F:norm():max(), + tostring(NEB:climbing(img))) ) + -- Prepare the relaxation for image `img` + local all_xa, weight = {}, flos.Array( #relax[img] ) + for i = 1, #relax[img] do + all_xa[i] = relax[img][i]:optimize(NEB[img].R, F) + weight[i] = relax[img][i].weight + end + weight = weight / weight:sum() + if #relax[img] > 1 then + IOprint("\n weighted average for relaxation: ", tostring(weight)) + end + -- Calculate the new coordinates and figure out + -- if the algorithm has converged (all forces below) + local out_xa = all_xa[1] * weight[1] + relaxed = relaxed and relax[img][1]:optimized() + for i = 2, #relax[img] do + out_xa = out_xa + all_xa[i] * weight[i] + relaxed = relaxed and relax[img][i]:optimized() + end + -- Copy the optimized coordinates to a table + --out_R[img] = out_xa + --================================================================- + -- For Lattice Optimization + --================================================================- + local icell = VCNEB[img].R --/ Unit.Ang + --local all_strain={} + local ivol=icell[1]:cross(icell[2]):dot(icell[3]) + local strain=flos.Array.zeros(6) + local stress_mask=flos.Array.ones(6) + stress_mask[3]=0.0 + stress_mask[4]=0.0 + stress_mask[5]=0.0 + stress_mask[6]=0.0 + local stress=-stress_to_voigt(siesta.geom.stress)--* Unit.Ang ^ 3 / Unit.eV + stress = stress * stress_mask + local VF = VCNEB:force(img, siesta.IONode) + IOprint("VCNEB: max Strain F on image ".. img .. + (" = %10.5f, climbing = %s"):format(VF:norm():max(), + tostring(VCNEB:climbing(img))) ) + IOprint(VCNEB[img].F) + local all_vcxa, vcweight = {}, flos.Array( #vcrelax[img] ) + for i = 1, #vcrelax[img] do + all_vcxa[i] = vcrelax[img][i]:optimize(strain, stress )--* ivol + vcweight[i] = vcrelax[img][i].weight + end + vcweight = vcweight / vcweight:sum() + if #vcrelax[img] > 1 then + IOprint("\n weighted average for cell relaxation: ", tostring(vcweight)) + end + -- Calculate the new coordinates and figure out + -- if the algorithm has converged (all forces below) + local out_vcxa = all_vcxa[1] * vcweight[1] + vcrelaxed = vcrelaxed and vcrelax[img][1]:optimized() + for i = 2, #relax[img] do + out_vcxa = out_vcxa + all_vcxa[i] * vcweight[i] + vcrelaxed = vcrelaxed and vcrelax[img][i]:optimized() + end + + --local out_strain=all_strain[1]*vcweight[1] + all_vcxa = nil --all_strain = nil + strain = out_vcxa * stress_mask --strain = out_strain * stress_mask + out_vcxa = nil --strain = out_strain * stress_mask --out_strain = nil + local dcell = flos.Array(icell.shape) + dcell[1][1]=1.0 + strain[1] + dcell[1][2]=0.5 * strain[6] + dcell[1][3]=0.5 * strain[5] + dcell[2][1]=0.5 * strain[6] + dcell[2][2]=1.0 + strain[2] + --dcell[2][2]=1.0 + strain[1] + dcell[2][3]=0.5 * strain[4] + dcell[3][1]=0.5 * strain[5] + dcell[3][2]=0.5 * strain[4] + dcell[3][3]=1.0 + strain[3] + local out_cell=icell:dot(dcell) + --local out_cell=icell+dcell + --print ("stress") + --print(stress) + --print("cell out") + --print (out_cell) + dcell = nil + local lat = flos.Lattice:new(icell) + local fxa = lat:fractional(out_xa) + xa =fxa:dot(out_cell) + lat = nil + fxa = nil + -- Copy the optimized vectors to a table + out_VR[img] = out_cell + -- Copy the optimized coordinates with respecto to new optimized vectors to a table + out_R[img] = xa + --================================================================-- + end + + -- Before we update the coordinates we will write + -- the current steps results to the result file + -- (this HAS to be done before updating the coordinates) + NEB:save( siesta.IONode ) + + -- Now we may copy over the coordinates (otherwise + -- we do a consecutive update, and then overwrite) + for img = 1, NEB.n_images do + NEB[img]:set{R=out_R[img]} + VCNEB[img]:set{R=out_VR[img]} + end + -- Start over in case the system has not relaxed + current_image = 1 + if relaxed and vcrelaxed then + tot_relax= true + -- the final coordinates are returned + siesta.geom.xa = NEB.final.R * Unit.Ang + siesta.geom.cell = VCNEB.final.R * Unit.Ang + IOprint("\nLUA/NEB complete\n") + else + siesta.geom.xa = NEB[1].R * Unit.Ang + siesta.geom.cell = VCNEB[1].R * Unit.Ang + IOprint(("\nLUA/NEB running NEB image %d / %d\n"):format(current_image, NEB.n_images)) + IOprint("Lattice Vectors") + IOprint(VCNEB[1].R) + IOprint("Stresss") + IOprint(VCNEB[1].F) + end + siesta.MD.Relaxed = tot_relax + return {"geom.xa","geom.stress","geom.cell", + "MD.Relaxed"} +end +--[[ +function file_exists(name) + local f = io.open(name, "r") + if f ~= nil then + io.close(f) + return true + else + return false + end +end--]] + +-- Function for retaining the DM files for the images so that we +-- can easily restart etc. +function siesta_update_DM(old, current) + + if not siesta.IONode then + -- only allow the IOnode to perform stuff... + return + end + -- Move about files so that we re-use old DM files + local DM = label .. ".DM" + local old_DM = DM .. "." .. tostring(old) + local current_DM = DM .. "." .. tostring(current) + local initial_DM = DM .. ".0" + local final_DM = DM .. ".".. tostring(NEB.n_images+1) + print ("The Label of Old DM is : " .. old_DM) + print ("The Label of Current DM is : " .. current_DM) + -- Saving initial DM + if old==0 and current==0 then + print("Removing DM for Resuming") + IOprint("Deleting " .. DM .. " for a clean restart...") + os.execute("rm " .. DM) + end + + if 0 <= old and old <= NEB.n_images+1 and NEB:file_exists(DM) then + -- store the current DM for restart purposes + IOprint("Saving " .. DM .. " to " .. old_DM) + os.execute("mv " .. DM .. " " .. old_DM) + elseif NEB:file_exists(DM) then + IOprint("Deleting " .. DM .. " for a clean restart...") + os.execute("rm " .. DM) + end + + if NEB:file_exists(current_DM) then + IOprint("Deleting " .. DM .. " for a clean restart...") + os.execute("rm " .. DM) + IOprint("Restoring " .. current_DM .. " to " .. DM) + os.execute("cp " .. current_DM .. " " .. DM) + end + +end + +function stress_to_voigt(stress) + local voigt = flos.Array.empty(6) + voigt[1]=stress[1][1] + voigt[2]=stress[2][2] + voigt[3]=stress[3][3] + voigt[4]=(stress[2][3]+stress[3][2])*0.5 + voigt[5]=(stress[1][3]+stress[3][1])*0.5 + voigt[6]=(stress[1][2]+stress[2][1])*0.5 + return voigt +end +function siesta_update_xyz(current) + if not siesta.IONode then + -- only allow the IOnode to perform stuff... + return + end + local xyz_label = f_label_xyz ..tostring(current)..".xyz" + --self:_n_images=self.n_images + --self:_check_image(image) + + local f=io.open(xyz_label,"w") + f:write(tostring(#NEB[current].R).."\n \n") + --f:write(tostring(initialize:self.n_images).."\n \n") + for i=1,#NEB[current].R do + f:write(string.format(" %19.17f",tostring(NEB[current].R[i][1])).. " "..string.format("%19.17f",tostring(NEB[current].R[i][2]))..string.format(" %19.17f",tostring(NEB[current].R[i][3])).."\n") + end + f:close() + -- +end + +function siesta_update_xyz_vec(current) + if not siesta.IONode then + -- only allow the IOnode to perform stuff... + return + end + local xyz_vec_label = f_label_xyz_vec ..tostring(current)..".xyz" + --self:_n_images=self.n_images + --self:_check_image(image) + + local f=io.open(xyz_vec_label,"w") + f:write(tostring(#VCNEB[current].R).."\n \n") + --f:write(tostring(initialize:self.n_images).."\n \n") + for i=1,#VCNEB[current].R do + f:write(string.format(" %19.17f",tostring(VCNEB[current].R[i][1])).. " "..string.format("%19.17f",tostring(VCNEB[current].R[i][2]))..string.format(" %19.17f",tostring(VCNEB[current].R[i][3])).."\n") + end + f:close() + -- +end