ROM Pinned H2O (#271)

* Reenable testShortSighted test (#248)

* Make new driver to check input (#247)

* clean up/reorganize main.cc
* use shared_ptr in class MGmol

* Add possible periodic dimensions to xyz2in.py (#249)

* Add possible periodic dimensions to xyz2in.py

* Remove unused/untested option extrapolateH (#250)

* Exit with failure if density off by more than 2% (#251)

* Exit with failure if density off by more than 2%
* adapt SiH4 test to catch that
* fix bug in DFTsolver that was leading to wrong density

* Example driver (#252)

* add example driver, showing use of MGmol as a force/energy computational engine

* clean up related functions in class Ions

* loadOrbitalsFromRestartFile -> loadRestartFile (#253)

* Add SG15 PBE potential for N (#258)

* Update 2-pyridone example (#259)

* Adjust verbosity in some functions (#260)

* Add new example: pinned H2O (#261)

* Print out eigenvalues out of MVP solver (#262)

Previously, the wrong eigenvalues (0) were printed out because eigenvalues outside solver were not up-to-date.

* Add Li2 example with local GTH potential (#263)

* Fix LBFGS termination when converged (#264)

* Remove unused code to extrapolate rho (#265)

* Fix and test EnergyAndForces interface (#266)

* Atomic potentials were not updated when atomic positions were changed
* Added test to make sure energies and forces are the same after positions
  move by one mesh spacing

* Add new functionality to compute energy and forces (#267)

* use specified initial conditions for wavefunctions

---------

Co-authored-by: Jean-Luc Fattebert <fattebertj@ornl.gov>
Co-authored-by: Kevin" Seung Whan Chung <seung.chung@austin.utexas.edu>

examples/2-pyridone/2-pyridone.cfg

@@ -1,5 +1,6 @@
 verbosity=1
 xcFunctional=PBE
+FDtype=4th
 [Mesh]
 nx=128
 ny=128
@@ -12,30 +13,17 @@ lx=24.
 ly=24.
 lz=12.
 [Potentials]
-pseudopotential=pseudo.N_soft_pbe
-pseudopotential=pseudo.O_pbe
-pseudopotential=pseudo.C_pbe
-pseudopotential=pseudo.H_pbe
-[Poisson]
-solver=MG
-max_steps_initial=10
-max_steps=10
-bcx=periodic
-bcy=periodic
-bcz=periodic
+pseudopotential=pseudo.N_ONCV_PBE_SG15
+pseudopotential=pseudo.O_ONCV_PBE_SG15
+pseudopotential=pseudo.C_ONCV_PBE_SG15
+pseudopotential=pseudo.H_ONCV_PBE_SG15
 [Run]
 type=QUENCH
 [Quench]
-step_length=1.5
 max_steps=200
 atol=1.e-7
-num_lin_iterations=2
-ortho_freq=20
-interval_print_residual=10
 [Orbitals]
 initial_type=Gaussian
 initial_width=1.5
-[ProjectedMatrices]
-solver=exact
-[Restart]
-output_type=single_file
+[Poisson]
+FDtype=4th

examples/2-pyridone/README

@@ -1,6 +1,6 @@
-ln -s ../../potentials/pseudo.N_soft_pbe
-ln -s ../../potentials/pseudo.O_pbe
-ln -s ../../potentials/pseudo.C_pbe
-ln -s ../../potentials/pseudo.H_pbe
+ln -s ../../potentials/pseudo.N_ONCV_PBE_SG15
+ln -s ../../potentials/pseudo.O_ONCV_PBE_SG15
+ln -s ../../potentials/pseudo.C_ONCV_PBE_SG15
+ln -s ../../potentials/pseudo.H_ONCV_PBE_SG15
 
-srun -ppdebug -n32 /nfs/tmp2/jeanluc/SVN/MGmol/mgmol/branches/bin/mgmol-pel -c 2-pyridone.cfg -l lrs.in -i coords.in
+srun -ppdebug -n32 mgmol-opt -c 2-pyridone.cfg -l lrs.in -i coords.in

examples/2-pyridone/coords.in

@@ -1,13 +1,12 @@
-N1	1	10.0818    7.9149   6.    1
-O1	2	14.2787    7.9126   6.    1
-C1	3	 7.9625    9.1867   6.    0
-C2	3	 7.8388   11.8070   6.    0
-C3	3	10.1050   13.1610   6.    0
-C4	3	12.3830   11.8680   6.    0
-C5	3	12.2810    9.2255   6.    0
-H1	4	 6.2219    8.0878   6.    1
-H2	4	 6.0028   12.7142   6.    1
-H3	4	10.0754   15.2192   6.    1
-H4	4	14.2295   12.7482   6.    1
-H5	4	10.2332    6.0038   6.    1
-
+N1	1	10.0818    7.9149   6.
+O1	2	14.2787    7.9126   6.
+C1	3	 7.9625    9.1867   6.
+C2	3	 7.8388   11.8070   6.
+C3	3	10.1050   13.1610   6.
+C4	3	12.3830   11.8680   6.
+C5	3	12.2810    9.2255   6.
+H1	4	 6.2219    8.0878   6.
+H2	4	 6.0028   12.7142   6.
+H3	4	10.0754   15.2192   6.
+H4	4	14.2295   12.7482   6.
+H5	4	10.2332    6.0038   6.

examples/Li2GTH/README

@@ -0,0 +1,11 @@
+#Run MGmol
+mpirun -np 4 mgmol-opt -c davidson.cfg -i li2.xyz > davidson.out
+
+#extract visit files from HDF5 file
+python read_hdf5.py -bov li2.h5 Vtotal
+
+python read_hdf5.py -bov li2.h50 Function0002
+
+Note: the eigenfunctions corresponding to the 3 occupied states are stored
+in functions 2, 3 and 4 because they are the result of diagonalizing the DM
+in Davidson algorithm, not H.

examples/Li2GTH/davidson.cfg

@@ -0,0 +1,46 @@
+verbosity=2
+xcFunctional=PBE
+FDtype=4th
+[Mesh]
+nx=96
+ny=96
+nz=96
+[Domain]
+ox=-9.
+oy=-9.
+oz=-9.
+lx=18.
+ly=18.
+lz=18.
+[Potentials]
+pseudopotential=pseudo.Li_GTH_PBE
+[Poisson]
+solver=CG
+bcx=0
+bcy=0
+bcz=0
+[Run]
+type=QUENCH
+[Quench]
+solver=Davidson
+max_steps=200
+atol=1.e-8
+preconditioner_num_levels=3
+[Orbitals]
+nempty=2
+initial_type=random
+temperature=300.
+bcx=0
+bcy=0
+bcz=0
+[ProjectedMatrices]
+solver=exact
+[DensityMatrix]
+nb_inner_it=1
+mixing=1.
+[Restart]
+output_level=3
+output_filename=li2.h5
+output_type=single_file
+[Coloring]
+scope=global

examples/Li2GTH/li2.xyz

@@ -0,0 +1,4 @@
+2
+Experimental geometry (Menconi and Tozer, Chem. Phys. Lett. 2002)
+Li  1.3365 0.0 0.0
+Li -1.3365 0.0 0.0

examples/PinnedH2O/README

@@ -0,0 +1,3 @@
+Single water molecule MD, with Oxigen atom pinned to (0,0,0) coordinate:
+
+mpirun -np 4 mgmol-opt -c mgmol.cfg -i coords.in

examples/PinnedH2O/coords.in

@@ -0,0 +1,3 @@
+O1  1   0.00    0.00    0.00  0
+H1  2  -0.45    1.42   -1.07  1
+H2  2  -0.45   -1.48   -0.97  1

examples/PinnedH2O/mgmol.cfg

@@ -0,0 +1,35 @@
+verbosity=1
+xcFunctional=PBE
+FDtype=Mehrstellen
+[Mesh]
+nx=64
+ny=64
+nz=64
+[Domain]
+ox=-6.
+oy=-6.
+oz=-6.
+lx=12.
+ly=12.
+lz=12.
+[Potentials]
+pseudopotential=pseudo.O_ONCV_PBE_SG15
+pseudopotential=pseudo.H_ONCV_PBE_SG15
+[Run]
+type=MD
+[MD]
+num_steps=50
+dt=40.
+thermostat=ON
+[Thermostat]
+type=Berendsen
+temperature=1000.
+relax_time=800.
+[Quench]
+max_steps=100
+atol=1.e-8
+[Orbitals]
+initial_type=Random
+initial_width=2.
+[Restart]
+output_level=0