diff --git a/potentials/pseudo.Br_ONCV_PBE_SG15 b/potentials/pseudo.Br_ONCV_PBE_SG15 new file mode 100644 index 00000000..c135617b --- /dev/null +++ b/potentials/pseudo.Br_ONCV_PBE_SG15 @@ -0,0 +1,2529 @@ +# This pseudopotential file has been produced using the code +# ONCVPSP (Optimized Norm-Conservinng Vanderbilt PSeudopotential) +# scalar-relativistic version 2.1.1, 03/26/2014 by D. R. Hamann +# The code is available through a link at URL www.mat-simresearch.com. +# Documentation with the package provides a full discription of the +# input data below. +# +# +# While it is not required under the terms of the GNU GPL, it is +# suggested that you cite D. R. Hamann, Phys. Rev. B 88, 085117 (2013) +# in any publication using these pseudopotentials. +# +# +# Copyright 2015 The Regents of the University of California +# +# This work is licensed under the Creative Commons Attribution-ShareAlike +# 4.0 International License. To view a copy of this license, visit +# http://creativecommons.org/licenses/by-sa/4.0/ or send a letter to +# Creative Commons, PO Box 1866, Mountain View, CA 94042, USA. +# +# This pseudopotential is part of the Schlipf-Gygi norm-conserving +# pseudopotential library. Its construction parameters were tuned to +# reproduce materials of a training set with very high accuracy and +# should be suitable as a general purpose pseudopotential to treat a +# variety of different compounds. For details of the construction and +# testing of the pseudopotential please refer to: +# +# M. Schlipf, F. Gygi, Comp. Phys. Comm. 196, 36 (2015) +# http://dx.doi.org/10.1016/j.cpc.2015.05.011 +# +# We kindly ask that you include this reference in all publications +# associated to this pseudopotential. +# +# +# Input file for PP generation: +# +# # ATOM AND REFERENCE CONFIGURATION +# # atsym z nc nv iexc psfile +# Br 35.00 6 2 4 fpmd +# # +# # n l f energy (Ha) +# 1 0 2.00 +# 2 0 2.00 +# 2 1 6.00 +# 3 0 2.00 +# 3 1 6.00 +# 3 2 10.00 +# 4 0 2.00 +# 4 1 5.00 +# # +# # PSEUDOPOTENTIAL AND OPTIMIZATION +# # lmax +# 2 +# # +# # l, rc, ep, ncon, nbas, qcut +# 0 2.49793 -0.73993 5 8 5.10687 +# 1 2.49793 -0.28884 5 8 4.46675 +# 2 2.49793 0.09432 5 8 4.91674 +# # +# # LOCAL POTENTIAL +# # lloc, lpopt, rc(5), dvloc0 +# 4 5 2.24365 0.00000 +# # +# # VANDERBILT-KLEINMAN-BYLANDER PROJECTORs +# # l, nproj, debl +# 0 2 1.26029 +# 1 2 1.41324 +# 2 2 1.05278 +# # +# # MODEL CORE CHARGE +# # icmod, fcfact +# 0 0.00000 +# # +# # LOG DERIVATIVE ANALYSIS +# # epsh1, epsh2, depsh +# -5.00 3.00 0.02 +# # +# # OUTPUT GRID +# # rlmax, drl +# 6.00 0.01 +# # +# # TEST CONFIGURATIONS +# # ncnf +# 0 +# # nvcnf +# # n l f +# +Br_ONCV_PBE +# +color +#radii of balls and covalent bonds +-1. -1. +# Nlcc flag +0 +# Atomic number +35 +# Atomic mass +79.90399933 +# Number of valence electrons +7 +#Gaussian core charge parameter rc +1.0 +# Number of potentials +4 +# l-value for state which is local, then type of potential format +3 3 +# Local potential radius +3.2 +# Non-local potential radius +3.2 +# number of points in radial grid +602 +# VANDERBILT-KLEINMAN-BYLANDER PROJECTORs +# l, nproj +0 2 -0.3626325499E+01 0.1750463805E+01 +1 2 0.4803824052E+02 0.7506916045E+00 +2 2 0.1514320363E+02 0.8114306630E-01 +# l= 0 +0.0 -3.0708154786 -2.4047930787 +0.01 -3.070772567 -2.4042133705 +0.02 -3.0706536405 -2.4024662354 +0.03 -3.0704488283 -2.3995597251 +0.04 -3.0701482591 -2.3955018914 +0.05 -3.0697381761 -2.3903039657 +0.06 -3.0692009986 -2.3839803178 +0.07 -3.0685154018 -2.376548404 +0.08 -3.0676564136 -2.3680287033 +0.09 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LIBROM_PATH=${BUILD_DIR}/libROM git clone https://github.com/LLNL/libROM cd libROM +git checkout 321d18f4d5adfa29f0a3de9be2699fee9732f2bf #./scripts/compile.sh -t ./cmake/toolchains/default-toss_4_x86_64_ib-librom-dev.cmake ./scripts/compile.sh cd ${BUILD_DIR} diff --git a/scripts/build_ubuntu22_openmpi.sh b/scripts/build_ubuntu22_openmpi.sh index a0ca470a..474d61e5 100755 --- a/scripts/build_ubuntu22_openmpi.sh +++ b/scripts/build_ubuntu22_openmpi.sh @@ -25,7 +25,7 @@ cmake -DCMAKE_INSTALL_PREFIX=${INSTALL_DIR} \ -DMPIEXEC_PREFLAGS="--oversubscribe" \ -DMGMOL_WITH_CLANG_FORMAT=ON \ -DCMAKE_PREFIX_PATH=${HOME}/bin \ - -DCMAKE_CXX_FLAGS="-Wall -pedantic -Wextra" \ + -D CMAKE_CXX_FLAGS="-Wall -pedantic -Wextra -Wno-cast-function-type" \ .. # call make install diff --git a/src/Control.cc b/src/Control.cc index 83fe2093..043e5640 100644 --- a/src/Control.cc +++ b/src/Control.cc @@ -31,23 +31,6 @@ float Control::total_spin_ = 0.; std::string Control::run_directory_("."); bool Control::with_spin_ = false; -static void finishRead(std::ifstream& tfile) -{ - // while( tfile.get()!='\n'); - // string str; - // getline(tfile,str); - char str[256]; - tfile.getline(str, 256); - - char cc = (char)tfile.peek(); - while (cc == ('#') || (cc == '\n') || cc == ' ') - { - while (tfile.get() != '\n') - ; - cc = (char)tfile.peek(); // look at next character - } -} - Control::Control() { assert(comm_global_ != MPI_COMM_NULL); @@ -1839,6 +1822,14 @@ int Control::checkOptions() return -1; } + if (DM_solver_ > 0 && lap_type == 0) + { + std::cerr << "DM_solver_ = " << DM_solver_ << std::endl; + std::cerr << "ERROR: Mehrstellen not compatible with MVP inner solvers!" + << std::endl; + return -1; + } + if (it_algo_type_ == 3 && lap_type == 0) { std::cerr diff --git a/src/Control.h b/src/Control.h index 162a68cc..a15bd24c 100644 --- a/src/Control.h +++ b/src/Control.h @@ -378,6 +378,8 @@ class Control // 10 or larger means CG, otherwise MG V-cycles bool MGPoissonSolver() { return (diel_flag_ / 10 == 0); } + bool LangevinThermostat() { return (thermostat_type == 1); } + // // data // diff --git a/src/DistributedIonicData.cc b/src/DistributedIonicData.cc index 6652c41a..05399cac 100644 --- a/src/DistributedIonicData.cc +++ b/src/DistributedIonicData.cc @@ -12,7 +12,6 @@ #include "tools.h" #include -using namespace std; DistributedIonicData::DistributedIonicData( const std::vector& local_names, @@ -31,16 +30,16 @@ DistributedIonicData::DistributedIonicData( int DistributedIonicData::pack(char* cbuff, double* dbuff) { - vector::iterator itf = data_.begin(); - double* dptr = dbuff; + std::vector::iterator itf = data_.begin(); + double* dptr = dbuff; int idx = 0; - for (vector::iterator it = ion_names_.begin(); + for (std::vector::iterator it = ion_names_.begin(); it != ion_names_.end(); ++it) { - string s(*it); + std::string s(*it); FixedLengthString t; - strncpy(t.mystring, s.c_str(), IonData_MaxStrLength); + strncpy(t.mystring, s.c_str(), IonData_MaxStrLength - 1); memcpy(&cbuff[idx], t.mystring, IonData_MaxStrLength); idx += IonData_MaxStrLength; @@ -58,7 +57,7 @@ void DistributedIonicData::unpack(char*& cptr, double*& dptr, const short ndata) for (short i = 0; i < ndata; i++) { // get name - string name(cptr, IonData_MaxStrLength); + std::string name(cptr, IonData_MaxStrLength); stripLeadingAndTrailingBlanks(name); ion_names_.push_back(name); cptr += IonData_MaxStrLength; diff --git a/src/HDFrestart.cc b/src/HDFrestart.cc index ef658955..0fac518e 100644 --- a/src/HDFrestart.cc +++ b/src/HDFrestart.cc @@ -428,7 +428,7 @@ void HDFrestart::addReleaseNumber2File(const char* release) // if( onpe0 ) { HDF_FixedLengthString t; - strncpy(t.mystring, release, MyHDFStrLength); + strncpy(t.mystring, release, MyHDFStrLength - 1); herr_t status = H5Awrite(attribute_id, strtype, &t); if (status < 0) { @@ -457,7 +457,8 @@ HDFrestart::HDFrestart(const std::string& filename, const pb::PEenv& pes, verbosity_ = 0; closed_ = false; - //(*MPIdata::sout)<<"HDFrestart::HDFrestart(), filename="<& data) +int HDFrestart::readAtomicData(std::string datasetname, std::vector& data) { Control& ct = *(Control::instance()); if (onpe0 && ct.verbose > 0) - { - (*MPIdata::sout) << "HDFrestart::readAtomicNumbers()..." << std::endl; - } + (*MPIdata::sout) << "HDFrestart::readAtomicData()..." << std::endl; if (active_) { assert(file_id_ >= 0); - htri_t exists = H5Lexists(file_id_, "/Atomic_numbers", H5P_DEFAULT); + htri_t exists = H5Lexists(file_id_, datasetname.c_str(), H5P_DEFAULT); if (!exists) return 0; // Open the dataset - hid_t dataset_id = H5Dopen2(file_id_, "/Atomic_numbers", H5P_DEFAULT); + hid_t dataset_id = H5Dopen2(file_id_, datasetname.c_str(), H5P_DEFAULT); if (dataset_id < 0) { - if (onpe0) - (*MPIdata::sout) - << "HDFrestart::readAtomicNumbers() --- H5Dopen2 failed!!!" - << std::endl; + MGMOL_HDFRESTART_FAIL("H5Dopen2 failed for " + datasetname); return -1; } int dim = (int)(H5Dget_storage_size(dataset_id) / sizeof(int)); if (dim == 0) { - if (onpe0) - (*MPIdata::sout) - << "HDFrestart::readAtomicNumbers() --- No numbers!!!" - << std::endl; + MGMOL_HDFRESTART_FAIL("No " + datasetname); return -1; } data.resize(dim); @@ -2017,174 +1909,52 @@ int HDFrestart::readAtomicNumbers(std::vector& data) H5P_DEFAULT, &data[0]); if (status < 0) { - (*MPIdata::sout) - << "HDFrestart::readAtomicNumbers() --- H5Dread failed!!!" - << std::endl; + MGMOL_HDFRESTART_FAIL("H5Dread failed for " + datasetname); return -1; } status = H5Dclose(dataset_id); if (status < 0) { - (*MPIdata::sout) - << "HDFrestart::readAtomicNumbers() --- H5Dclose failed!!!" - << std::endl; + MGMOL_HDFRESTART_FAIL("H5Dclose failed for " + datasetname); return -1; } } // if active_ // send data to inactive PEs if (gather_data_x_) gatherDataXdir(data); - return 0; -} - -// return -2 means failure -// return -1 means dataset does not exists, and could be from older MGmol -// version -int HDFrestart::readAtomicIDs(std::vector& data) -{ - Control& ct = *(Control::instance()); - if (onpe0 && ct.verbose > 0) - (*MPIdata::sout) << "HDFrestart::readAtomicIDs()..." << std::endl; - - if (active_) + if (useHdf5p()) { - assert(file_id_ >= 0); - htri_t exists = H5Lexists(file_id_, "/Atomic_IDs", H5P_DEFAULT); - if (!exists) return -1; - - // Open the dataset - hid_t dataset_id = H5Dopen2(file_id_, "/Atomic_IDs", H5P_DEFAULT); - if (dataset_id < 0) - { - if (onpe0) - (*MPIdata::sout) - << "HDFrestart::readAtomicIDs() --- H5Dopen2 failed!!!" - << std::endl; - return -2; - } - - int dim = (int)(H5Dget_storage_size(dataset_id) / sizeof(int)); - if (dim == 0) - { - if (onpe0) - (*MPIdata::sout) - << "HDFrestart::readAtomicIDs() --- No IDs!!!" << std::endl; - return -2; - } - data.resize(dim); - - herr_t status = H5Dread(dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, - H5P_DEFAULT, &data[0]); - if (status < 0) - { - (*MPIdata::sout) - << "HDFrestart::readAtomicIDs() --- H5Dread failed!!!" - << std::endl; - return -2; - } - status = H5Dclose(dataset_id); - if (status < 0) - { - (*MPIdata::sout) - << "HDFrestart::readAtomicIDs() --- H5Dclose failed!!!" - << std::endl; - return -2; - } + data.erase(std::remove(data.begin(), data.end(), -1), data.end()); } - if (gather_data_x_) gatherDataXdir(data); return 0; } -// return -2 means failure -// return -1 means dataset does not exists, and could be from older MGmol -// version -int HDFrestart::readAtomicNLprojIDs(std::vector& data) -{ - Control& ct = *(Control::instance()); - if (onpe0 && ct.verbose > 0) - (*MPIdata::sout) << "HDFrestart::readAtomicNLprojIDs()..." << std::endl; - - if (active_) - { - assert(file_id_ >= 0); - - htri_t exists = H5Lexists(file_id_, "/AtomicNLproj_IDs", H5P_DEFAULT); - if (!exists) return -1; - - hid_t dataset_id = H5Dopen2(file_id_, "/AtomicNLproj_IDs", H5P_DEFAULT); - if (dataset_id < 0) - { - if (onpe0) - (*MPIdata::sout) << "HDFrestart::readAtomicNLprojIDs() --- " - "H5Dopen2 failed!!!" - << std::endl; - return -2; - } - - int dim = (int)(H5Dget_storage_size(dataset_id) / sizeof(int)); - if (dim == 0) - { - if (onpe0) - (*MPIdata::sout) - << "HDFrestart::readAtomicNLprojIDs() --- No IDs!!!" - << std::endl; - return -2; - } - data.resize(dim); - - herr_t status = H5Dread(dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, - H5P_DEFAULT, &data[0]); - if (status < 0) - { - (*MPIdata::sout) - << "HDFrestart::readAtomicNLprojIDs() --- H5Dread failed!!!" - << std::endl; - return -2; - } - status = H5Dclose(dataset_id); - if (status < 0) - { - (*MPIdata::sout) - << "HDFrestart::readAtomicNLprojIDs() --- H5Dclose failed!!!" - << std::endl; - return -2; - } - } - - if (gather_data_x_) gatherDataXdir(data); - return 0; -} - -int HDFrestart::readAtomicPositions(std::vector& data) +int HDFrestart::readAtomicData( + std::string datasetname, std::vector& data) { if (onpe0) - (*MPIdata::sout) << "Read ionic positions from hdf5 file" << std::endl; + (*MPIdata::sout) << "Read atomic data from hdf5 file" << std::endl; if (active_) { assert(file_id_ >= 0); - htri_t exists = H5Lexists(file_id_, "/Ionic_positions", H5P_DEFAULT); + htri_t exists = H5Lexists(file_id_, datasetname.c_str(), H5P_DEFAULT); if (!exists) return -1; // Open the dataset - hid_t dataset_id = H5Dopen2(file_id_, "/Ionic_positions", H5P_DEFAULT); + hid_t dataset_id = H5Dopen2(file_id_, datasetname.c_str(), H5P_DEFAULT); if (dataset_id < 0) { - (*MPIdata::sout) - << "HDFrestart:readAtomicPositions() --- H5Dopen2 failed!!!" - << std::endl; + MGMOL_HDFRESTART_FAIL("H5Dopen2 failed for " + datasetname); return -2; } int dim = (int)H5Dget_storage_size(dataset_id) / sizeof(double); if (dim == 0) { - if (onpe0) - (*MPIdata::sout) - << "HDFrestart:readAtomicPositions() --- No positions!!!" - << std::endl; + MGMOL_HDFRESTART_FAIL("readAtomicData() --- No " + datasetname); return -2; } data.resize(dim); @@ -2193,19 +1963,21 @@ int HDFrestart::readAtomicPositions(std::vector& data) H5P_DEFAULT, &data[0]); if (status < 0) { - (*MPIdata::sout) - << "HDFrestart:readAtomicPositions() --- H5Dread failed!!!" - << std::endl; + MGMOL_HDFRESTART_FAIL("H5Dread failed for " + datasetname); return -2; } status = H5Dclose(dataset_id); if (status < 0) { - (*MPIdata::sout) << "H5Dclose failed!!!" << std::endl; + MGMOL_HDFRESTART_FAIL("H5Dclose failed for " + datasetname); return -2; } } + if (useHdf5p()) + { + data.erase(std::remove(data.begin(), data.end(), 1e+32), data.end()); + } if (gather_data_x_) gatherDataXdir(data); return 0; @@ -2218,59 +1990,12 @@ int HDFrestart::readOldCenterOnMesh(std::vector& data, int i) "points from hdf5 file" << std::endl; - if (active_) - { - assert(file_id_ >= 0); - - std::stringstream datasetstream; - datasetstream << "OldCenterOnMesh_" << i; - - std::string datasetname = datasetstream.str(); - - htri_t exists = H5Lexists(file_id_, datasetname.c_str(), H5P_DEFAULT); - if (!exists) return -1; - - // Open the dataset - hid_t dataset_id = H5Dopen2(file_id_, datasetname.c_str(), H5P_DEFAULT); - if (dataset_id < 0) - { - (*MPIdata::sout) - << "HDFrestart:readOldCenterOnMesh() --- H5Dopen2 failed!!!" - << std::endl; - return -2; - } - - int dim = (int)H5Dget_storage_size(dataset_id) / sizeof(double); - if (dim == 0) - { - if (onpe0) - (*MPIdata::sout) - << "HDFrestart:readOldCenterOnMesh() --- No old centers!!!" - << std::endl; - return -2; - } - data.resize(dim); - - herr_t status = H5Dread(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, - H5P_DEFAULT, &data[0]); - if (status < 0) - { - (*MPIdata::sout) - << "HDFrestart:readOldCenterOnMesh() --- H5Dread failed!!!" - << std::endl; - return -2; - } - status = H5Dclose(dataset_id); - if (status < 0) - { - (*MPIdata::sout) << "H5Dclose failed!!!" << std::endl; - return -2; - } - } + std::stringstream datasetstream; + datasetstream << "OldCenterOnMesh_" << i; - if (gather_data_x_) gatherDataXdir(data); + std::string datasetname = datasetstream.str(); - return 0; + return readAtomicData(datasetname, data); } int HDFrestart::readOldCenter(std::vector& data, int i) @@ -2279,256 +2004,16 @@ int HDFrestart::readOldCenter(std::vector& data, int i) (*MPIdata::sout) << "Read old localization centers from hdf5 file" << std::endl; - if (active_) - { - assert(file_id_ >= 0); + std::stringstream datasetstream; + datasetstream << "OldCenter_" << i; - std::stringstream datasetstream; - datasetstream << "OldCenter_" << i; + std::string datasetname = datasetstream.str(); - std::string datasetname = datasetstream.str(); - - htri_t exists = H5Lexists(file_id_, datasetname.c_str(), H5P_DEFAULT); - if (!exists) return -1; - - // Open the dataset - hid_t dataset_id = H5Dopen2(file_id_, datasetname.c_str(), H5P_DEFAULT); - if (dataset_id < 0) - { - (*MPIdata::sout) - << "HDFrestart:readOldCenter() --- H5Dopen2 failed!!!" - << std::endl; - return -2; - } - - int dim = (int)H5Dget_storage_size(dataset_id) / sizeof(double); - if (dim == 0) - { - if (onpe0) - (*MPIdata::sout) - << "HDFrestart:readOldCenter() --- No old centers!!!" - << std::endl; - return -2; - } - data.resize(dim); - - herr_t status = H5Dread(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, - H5P_DEFAULT, &data[0]); - if (status < 0) - { - (*MPIdata::sout) - << "HDFrestart:readOldCenter() --- H5Dread failed!!!" - << std::endl; - return -2; - } - status = H5Dclose(dataset_id); - if (status < 0) - { - (*MPIdata::sout) << "H5Dclose failed!!!" << std::endl; - return -2; - } - } - - if (gather_data_x_) gatherDataXdir(data); - - return 0; -} - -int HDFrestart::readGidsList(std::vector& data) -{ - if (onpe0) - (*MPIdata::sout) << "Read list of gids from hdf5 file" << std::endl; - - if (active_) - { - assert(file_id_ >= 0); - - std::string datasetname = "GidsList"; - - htri_t exists = H5Lexists(file_id_, datasetname.c_str(), H5P_DEFAULT); - if (!exists) return -1; - - // Open the dataset - hid_t dataset_id = H5Dopen2(file_id_, datasetname.c_str(), H5P_DEFAULT); - if (dataset_id < 0) - { - (*MPIdata::sout) - << "HDFrestart:readGidsList() --- H5Dopen2 failed!!!" - << std::endl; - return -2; - } - - int dim = (int)H5Dget_storage_size(dataset_id) / sizeof(int); - if (dim == 0) - { - if (onpe0) - (*MPIdata::sout) - << "HDFrestart:readGidsList() --- No GidsList!!!" - << std::endl; - return -2; - } - data.resize(dim); - - herr_t status = H5Dread(dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, - H5P_DEFAULT, &data[0]); - if (status < 0) - { - (*MPIdata::sout) - << "HDFrestart:readGidsList() --- H5Dread failed!!!" - << std::endl; - return -2; - } - status = H5Dclose(dataset_id); - if (status < 0) - { - (*MPIdata::sout) << "H5Dclose failed!!!" << std::endl; - return -2; - } - } - - if (gather_data_x_) gatherDataXdir(data); - - return 0; -} - -int HDFrestart::readAtomicVelocities(std::vector& data) -{ - if (onpe0) - (*MPIdata::sout) << "Read atomic velocities from hdf5 file" - << std::endl; - - if (active_) - { - assert(file_id_ >= 0); - - htri_t exists = H5Lexists(file_id_, "/Ionic_velocities", H5P_DEFAULT); - if (exists) - { - - // Open an existing dataset - hid_t dataset_id - = H5Dopen2(file_id_, "/Ionic_velocities", H5P_DEFAULT); - if (dataset_id < 0) - { - std::cerr << "HDFrestart::readAtomicVelocities(), " - "H5Dopen failed->no velocities read" - << std::endl; - data.clear(); - return -1; - } - int dim = (int)H5Dget_storage_size(dataset_id) / sizeof(double); - data.resize(dim); - - herr_t status = H5Dread(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, - H5S_ALL, H5P_DEFAULT, &data[0]); - if (status < 0) - { - MGMOL_HDFRESTART_FAIL("H5Dread failed!!!"); - return -2; - } - - status = H5Dclose(dataset_id); - if (status < 0) - { - MGMOL_HDFRESTART_FAIL("H5Dclose failed!!!"); - return -2; - } - } - } - - if (gather_data_x_) gatherDataXdir(data); - - return 0; -} - -int HDFrestart::readLockedAtomNames(std::vector& data) -{ - if (onpe0) - (*MPIdata::sout) << "HDFrestart::readLockedAtomNames()..." << std::endl; - - std::vector buffer; - short name_length = 7; // default, value used before February 2016 - - if (active_) - { - assert(file_id_ >= 0); - - htri_t exists = H5Lexists(file_id_, "/LockedAtomsNames", H5P_DEFAULT); - if (!exists) return 0; - - hid_t dataset_id = H5Dopen2(file_id_, "/LockedAtomsNames", H5P_DEFAULT); - if (dataset_id < 0) - { - if (onpe0) - (*MPIdata::sout) << "HDFrestart::readLockedAtomNames(), " - "H5Dopen failed->no locked atoms read" - << std::endl; - return -1; - } - - std::string attname("String_Length"); - htri_t existsA = H5Aexists(dataset_id, attname.c_str()); - if (existsA) - { - hid_t attribute_id = H5Aopen_name(dataset_id, attname.c_str()); - herr_t status = H5Aread(attribute_id, H5T_NATIVE_INT, &name_length); - // check validity of data just read - if (status < 0) - { - MGMOL_HDFRESTART_FAIL("H5Aread failed!!!"); - return -1; - } - } - - int dim = (int)H5Dget_storage_size(dataset_id) / name_length; - - if (onpe0) - (*MPIdata::sout) - << "HDFrestart::readLockedAtomNames(), dataset size=" << dim - << std::endl; - - if (dim == 0) return 0; - - buffer.resize(dim * name_length); - - // create type for std::strings of length IonData_MaxStrLength - hid_t strtype = H5Tcopy(H5T_C_S1); - H5Tset_size(strtype, name_length); - herr_t status = H5Dread( - dataset_id, strtype, H5S_ALL, H5S_ALL, H5P_DEFAULT, &buffer[0]); - if (status < 0) - { - (*MPIdata::sout) - << "HDFrestart::readLockedAtomNames(), H5Dread failed!!!" - << std::endl; - return -1; - } - status = H5Dclose(dataset_id); - if (status < 0) - { - (*MPIdata::sout) << "H5Dclose failed!!!" << std::endl; - return -1; - } - } - - if (gather_data_x_) gatherDataXdir(buffer); - - data.clear(); - for (unsigned short i = 0; i < buffer.size(); i += name_length) - { - std::string t(&buffer[i], name_length); - assert(t.size() > 0); - - stripLeadingAndTrailingBlanks(t); - - assert(t.size() > 0); - data.push_back(t); - } - - return 0; + return readAtomicData(datasetname, data); } -int HDFrestart::readAtomicNames(std::vector& data) +int HDFrestart::readAtomicData( + std::string datasetname, std::vector& data) { Control& ct = *(Control::instance()); if (onpe0 && ct.verbose > 0) @@ -2541,11 +2026,12 @@ int HDFrestart::readAtomicNames(std::vector& data) { assert(file_id_ >= 0); - htri_t exists = H5Lexists(file_id_, "/Atomic_names", H5P_DEFAULT); + htri_t exists = H5Lexists(file_id_, datasetname.c_str(), H5P_DEFAULT); if (exists) { // Open the dataset - hid_t dataset_id = H5Dopen2(file_id_, "/Atomic_names", H5P_DEFAULT); + hid_t dataset_id + = H5Dopen2(file_id_, datasetname.c_str(), H5P_DEFAULT); if (dataset_id < 0) { MGMOL_HDFRESTART_FAIL("H5Dopen2 failed!!!"); @@ -2577,7 +2063,7 @@ int HDFrestart::readAtomicNames(std::vector& data) int dim = (int)H5Dget_storage_size(dataset_id) / name_length; if (dim == 0) { - if (onpe0) MGMOL_HDFRESTART_FAIL("No names!!!"); + MGMOL_HDFRESTART_FAIL("No names!!!"); return -1; } @@ -2618,6 +2104,11 @@ int HDFrestart::readAtomicNames(std::vector& data) data.push_back(t); } + if (useHdf5p()) + { + data.erase(std::remove(data.begin(), data.end(), ""), data.end()); + } + return 0; } @@ -2652,7 +2143,6 @@ int HDFrestart::readRestartRandomStates(std::vector& data) dim = (int)H5Dget_storage_size(dataset_id) / sizeof(unsigned short); } - if (dim > 0) { data.resize(dim); @@ -2672,12 +2162,10 @@ int HDFrestart::readRestartRandomStates(std::vector& data) } if (!data.empty()) - if (data[0] != data[0]) + if (std::isnan(data[0])) { MGMOL_HDFRESTART_FAIL( - "ERROR: HDFrestart::readRestartRandomStates() " - "--- data[0]=" - << data[0]); + "readRestartRandomStates() is NaN"); return -2; } } diff --git a/src/HDFrestart.h b/src/HDFrestart.h index 72c5c1f5..1ed2d080 100644 --- a/src/HDFrestart.h +++ b/src/HDFrestart.h @@ -260,19 +260,12 @@ class HDFrestart template int readData(T* vv, hid_t memspace, hid_t dset_id, const short precision); - // int writeRandomState(unsigned short int rand_state[3]); - // int readRandomState(unsigned short* rand_state); - int readAtomicIDs(std::vector& data); - int readAtomicNLprojIDs(std::vector& data); - int readAtomicNumbers(std::vector& data); - int readAtomicNames(std::vector& data); - int readAtomicPositions(std::vector& data); - int readAtomicVelocities(std::vector& data); - int readLockedAtomNames(std::vector& data); + int readAtomicData(std::string datasetname, std::vector& data); + int readAtomicData(std::string datasetname, std::vector& data); + int readAtomicData(std::string datasetname, std::vector& data); int readRestartRandomStates(std::vector& data); int readOldCenter(std::vector& data, int i); int readOldCenterOnMesh(std::vector& data, int i); - int readGidsList(std::vector& data); void addDateToFilename(); void addMDTime2File(const float run_time); diff --git a/src/HamiltonianMVP_DMStrategy.cc b/src/HamiltonianMVP_DMStrategy.cc index 2b5f8913..be62b894 100644 --- a/src/HamiltonianMVP_DMStrategy.cc +++ b/src/HamiltonianMVP_DMStrategy.cc @@ -57,7 +57,7 @@ HamiltonianMVP_DMStrategy void HamiltonianMVP_DMStrategy::initialize(OrbitalsType& orbitals) + OrbitalsType>::initialize(OrbitalsType&) { } diff --git a/src/Ion.h b/src/Ion.h index 336dee72..ae870820 100644 --- a/src/Ion.h +++ b/src/Ion.h @@ -176,7 +176,7 @@ class Ion } double position(const short i) const { return position_[i]; } - double old_position(const short i) const { return old_position_[i]; } + double getPreviousPosition(const short i) const { return old_position_[i]; } void setPosition(const double x, const double y, const double z) { old_position_[0] = position_[0]; diff --git a/src/IonData.cc b/src/IonData.cc index 8f62ddd8..89c1bd0c 100644 --- a/src/IonData.cc +++ b/src/IonData.cc @@ -10,12 +10,11 @@ #include "IonData.h" #include "tools.h" #include -using namespace std; void IonData::unpack(char*& cptr, int*& iptr, double*& dptr) { // get name - string name(cptr, IonData_MaxStrLength); + std::string name(cptr, IonData_MaxStrLength); stripLeadingAndTrailingBlanks(name); ion_name = name; cptr += IonData_MaxStrLength; @@ -52,16 +51,16 @@ void IonData::unpack(char*& cptr, int*& iptr, double*& dptr) // pack Ions data for communication void IonData::packIonData( - char* cbuff, int* ibuff, double* dbuff, vector& data) + char* cbuff, int* ibuff, double* dbuff, std::vector& data) { // pack ion_names buffer int idx = 0; - for (vector::iterator idata = data.begin(); idata != data.end(); - ++idata) + for (std::vector::iterator idata = data.begin(); + idata != data.end(); ++idata) { - string s = (*idata).ion_name; + std::string s = (*idata).ion_name; FixedLengthString t; - strncpy(t.mystring, s.c_str(), IonData_MaxStrLength); + strncpy(t.mystring, s.c_str(), IonData_MaxStrLength - 1); memcpy(&cbuff[idx], t.mystring, IonData_MaxStrLength); idx += IonData_MaxStrLength; } @@ -69,8 +68,8 @@ void IonData::packIonData( // pack integer datatypes int* iptr = &ibuff[0]; // first pack local data size - *(iptr++) = data.size(); - vector::iterator idata = data.begin(); + *(iptr++) = data.size(); + std::vector::iterator idata = data.begin(); while (idata != data.end()) { // pack atomic_num diff --git a/src/IonicStepper.cc b/src/IonicStepper.cc index ca8d53cc..aa3a7f48 100644 --- a/src/IonicStepper.cc +++ b/src/IonicStepper.cc @@ -13,8 +13,6 @@ #include "MGmol_blas1.h" #include -using namespace std; - IonicStepper::IonicStepper(const double dt, const std::vector& atmove, std::vector& tau0, std::vector& taup) : atmove_(atmove), tau0_(tau0), taup_(taup) @@ -51,7 +49,8 @@ IonicStepper::IonicStepper(const double dt, const std::vector& atmove, } int IonicStepper::writeAtomicFields(HDFrestart& h5f_file, - const vector& data, const string& name, const bool create) const + const std::vector& data, const std::string& name, + const bool create) const { hid_t file_id = h5f_file.file_id(); if (file_id < 0) return 0; @@ -62,7 +61,6 @@ int IonicStepper::writeAtomicFields(HDFrestart& h5f_file, if (create) { - // Create the data space for new datasets hsize_t dims[2] = { (hsize_t)data.size() / 3, 3 }; dataspace_id = H5Screate_simple(2, dims, nullptr); @@ -70,7 +68,7 @@ int IonicStepper::writeAtomicFields(HDFrestart& h5f_file, { (*MPIdata::serr) << "IonicStepper::writeAtomicFields, H5Screate_simple failed!!!" - << endl; + << std::endl; return -1; } @@ -81,7 +79,7 @@ int IonicStepper::writeAtomicFields(HDFrestart& h5f_file, { (*MPIdata::serr) << "IonicStepper::writeAtomicFields, H5Dcreate2 " "failed for dataset " - << name << "!!!" << endl; + << name << "!!!" << std::endl; return -1; } } @@ -93,7 +91,7 @@ int IonicStepper::writeAtomicFields(HDFrestart& h5f_file, { (*MPIdata::serr) << "IonicStepper::writeAtomicFields, H5Dopen2 " "failed for dataset " - << name << "!!!" << endl; + << name << "!!!" << std::endl; return -1; } } @@ -103,7 +101,7 @@ int IonicStepper::writeAtomicFields(HDFrestart& h5f_file, if (status < 0) { (*MPIdata::serr) << "IonicStepper::writeAtomicFields: H5Dwrite " << name - << " failed!!!" << endl; + << " failed!!!" << std::endl; return -1; } else @@ -111,14 +109,15 @@ int IonicStepper::writeAtomicFields(HDFrestart& h5f_file, if (onpe0) (*MPIdata::sout) << "IonicStepper::writeAtomicFields, Data written into file " - << h5f_file.filename() << endl; + << h5f_file.filename() << std::endl; } status = H5Dclose(dataset_id); if (status < 0) { (*MPIdata::serr) - << "IonicStepper::writeAtomicFields, H5Dclose failed!!!" << endl; + << "IonicStepper::writeAtomicFields, H5Dclose failed!!!" + << std::endl; return -1; } @@ -129,7 +128,7 @@ int IonicStepper::writeAtomicFields(HDFrestart& h5f_file, { (*MPIdata::serr) << "IonicStepper::writeAtomicFields, H5Sclose failed!!!" - << endl; + << std::endl; return -1; } } @@ -137,7 +136,8 @@ int IonicStepper::writeAtomicFields(HDFrestart& h5f_file, return 0; } -int IonicStepper::writePositions(HDFrestart& h5f_file, const string& name) const +int IonicStepper::writePositions( + HDFrestart& h5f_file, const std::string& name) const { return writeAtomicFields(h5f_file, tau0_, name, false); } @@ -155,7 +155,8 @@ int IonicStepper::writeVelocities(HDFrestart& h5f_file) const hid_t dataspace_id = H5Screate_simple(2, dims, nullptr); if (dataspace_id < 0) { - (*MPIdata::serr) << "IonicStepper: H5Screate_simple failed!!!" << endl; + (*MPIdata::serr) << "IonicStepper: H5Screate_simple failed!!!" + << std::endl; return -1; } @@ -170,7 +171,7 @@ int IonicStepper::writeVelocities(HDFrestart& h5f_file) const { std::cerr << "IonicStepper::writeVelocities, H5Dopen2 " "failed for dataset " - << name << "!!!" << endl; + << name << "!!!" << std::endl; return -1; } } @@ -182,12 +183,12 @@ int IonicStepper::writeVelocities(HDFrestart& h5f_file) const { (*MPIdata::serr) << "IonicStepper:: H5Dcreate2 /Ionic_velocities failed!!!" - << endl; + << std::endl; return -1; } } - vector data(taup_); + std::vector data(taup_); double minus = -1.; int n = (int)tau0_.size(), ione = 1; DAXPY(&n, &minus, &tau0_[0], &ione, &data[0], &ione); @@ -202,20 +203,20 @@ int IonicStepper::writeVelocities(HDFrestart& h5f_file) const if (status < 0) { (*MPIdata::serr) << "IonicStepper::H5Dwrite velocities failed!!!" - << endl; + << std::endl; return -1; } else { if (onpe0) (*MPIdata::sout) << "Ionic velocities written into " - << h5f_file.filename() << endl; + << h5f_file.filename() << std::endl; } status = H5Dclose(dataset_id); if (status < 0) { - (*MPIdata::serr) << "H5Dclose failed!!!" << endl; + (*MPIdata::serr) << "H5Dclose failed!!!" << std::endl; return -1; } H5Sclose(dataspace_id); @@ -224,7 +225,7 @@ int IonicStepper::writeVelocities(HDFrestart& h5f_file) const } int IonicStepper::readAtomicFields( - HDFrestart& h5f_file, vector& data, const string& name) + HDFrestart& h5f_file, std::vector& data, const std::string& name) { hid_t file_id = h5f_file.file_id(); @@ -239,7 +240,7 @@ int IonicStepper::readAtomicFields( if (dataset_id < 0) { (*MPIdata::serr) << "IonicStepper, H5Dopen2 failed for " << name - << " !!!" << endl; + << " !!!" << std::endl; return -1; } @@ -249,14 +250,15 @@ int IonicStepper::readAtomicFields( H5S_ALL, H5P_DEFAULT, &data[0]); if (status < 0) { - (*MPIdata::serr) << "IonicStepper, H5Dread failed!!!" << endl; + (*MPIdata::serr) + << "IonicStepper, H5Dread failed!!!" << std::endl; return -1; } // close dataset status = H5Dclose(dataset_id); if (status < 0) { - (*MPIdata::serr) << "H5Dclose failed!!!" << endl; + (*MPIdata::serr) << "H5Dclose failed!!!" << std::endl; return -1; } } @@ -265,13 +267,14 @@ int IonicStepper::readAtomicFields( return 0; } -int IonicStepper::readPositions_hdf5(HDFrestart& h5f_file, const string& name) +int IonicStepper::readPositions_hdf5( + HDFrestart& h5f_file, const std::string& name) { return readAtomicFields(h5f_file, tau0_, name); } int IonicStepper::writeRandomStates(HDFrestart& h5f_file, - vector& data, const string& name) const + std::vector& data, const std::string& name) const { hid_t file_id = h5f_file.file_id(); bool create = false; @@ -282,7 +285,7 @@ int IonicStepper::writeRandomStates(HDFrestart& h5f_file, if (dataset_id < 0) { (*MPIdata::serr) << "IonicStepper:: H5Dopen2 " << name - << " failed!!! Creating new data file " << endl; + << " failed!!! Creating new data file " << std::endl; // Create the data space for the dataset hsize_t dims[2] = { (hsize_t)data.size() / 3, 3 }; @@ -291,7 +294,7 @@ int IonicStepper::writeRandomStates(HDFrestart& h5f_file, { (*MPIdata::serr) << "Ions::writeRandomStates: H5Screate_simple failed!!!" - << endl; + << std::endl; return -1; } // Create the dataset @@ -300,7 +303,7 @@ int IonicStepper::writeRandomStates(HDFrestart& h5f_file, if (dataset_id < 0) { (*MPIdata::serr) - << "Ions::writeRandomStates: H5Dcreate2 failed!!!" << endl; + << "Ions::writeRandomStates: H5Dcreate2 failed!!!" << std::endl; return -1; } create = true; @@ -312,7 +315,7 @@ int IonicStepper::writeRandomStates(HDFrestart& h5f_file, if (status < 0) { (*MPIdata::serr) << "IonicStepper::writeRandomStates: H5Dwrite " << name - << " failed!!!" << endl; + << " failed!!!" << std::endl; return -1; } else @@ -320,14 +323,15 @@ int IonicStepper::writeRandomStates(HDFrestart& h5f_file, if (onpe0) (*MPIdata::sout) << "IonicStepper::writeRandomStates, Data written into file " - << h5f_file.filename() << endl; + << h5f_file.filename() << std::endl; } status = H5Dclose(dataset_id); if (status < 0) { (*MPIdata::serr) - << "IonicStepper::writeRandomStates, H5Dclose failed!!!" << endl; + << "IonicStepper::writeRandomStates, H5Dclose failed!!!" + << std::endl; return -1; } @@ -338,7 +342,7 @@ int IonicStepper::writeRandomStates(HDFrestart& h5f_file, { (*MPIdata::serr) << "IonicStepper::writeAtomicFields, H5Sclose failed!!!" - << endl; + << std::endl; return -1; } } @@ -346,8 +350,8 @@ int IonicStepper::writeRandomStates(HDFrestart& h5f_file, return 0; } -int IonicStepper::readRandomStates( - HDFrestart& h5f_file, vector& data, const string& name) +int IonicStepper::readRandomStates(HDFrestart& h5f_file, + std::vector& data, const std::string& name) { hid_t file_id = h5f_file.file_id(); @@ -360,10 +364,10 @@ int IonicStepper::readRandomStates( if (onpe0) { (*MPIdata::sout) - << "H5Dopen failed for /Ionic_RandomStates" << endl; + << "H5Dopen failed for /Ionic_RandomStates" << std::endl; (*MPIdata::sout) << "Set random states to default computed in Ion.cc" - << endl; + << std::endl; } } else @@ -373,19 +377,20 @@ int IonicStepper::readRandomStates( if (onpe0) (*MPIdata::sout) << "Read Ionic random states from " - << h5f_file.filename() << endl; + << h5f_file.filename() << std::endl; herr_t status = H5Dread(dataset_id, H5T_NATIVE_USHORT, H5S_ALL, H5S_ALL, H5P_DEFAULT, &data[0]); if (status < 0) { - (*MPIdata::serr) << "IonicStepper: H5Dread failed!!!" << endl; + (*MPIdata::serr) + << "IonicStepper: H5Dread failed!!!" << std::endl; return -1; } // close dataset status = H5Dclose(dataset_id); if (status < 0) { - (*MPIdata::serr) << "H5Dclose failed!!!" << endl; + (*MPIdata::serr) << "H5Dclose failed!!!" << std::endl; return -1; } } diff --git a/src/Ions.cc b/src/Ions.cc index 852151c7..e93d82ea 100644 --- a/src/Ions.cc +++ b/src/Ions.cc @@ -34,13 +34,13 @@ Timer ions_setup_tm("ions::setup"); const double ang2bohr = 1.8897269; // const double rmax = 8.0; -std::map Ions::map_species_ - = { { "H", 1 }, { "D", 1 }, { "Li", 3 }, { "Be", 4 }, { "B", 5 }, - { "C", 6 }, { "N", 7 }, { "O", 8 }, { "F", 9 }, { "Na", 11 }, - { "Mg", 12 }, { "Al", 13 }, { "Si", 14 }, { "P", 15 }, { "S", 16 }, - { "Cl", 17 }, { "K", 19 }, { "Ca", 20 }, { "Cr", 24 }, { "Mn", 25 }, - { "Fe", 26 }, { "Co", 27 }, { "Ni", 28 }, { "Cu", 29 }, { "Zn", 30 }, - { "Ga", 31 }, { "Ge", 32 }, { "La", 57 }, { "Au", 79 } }; +std::map Ions::map_species_ = { { "H", 1 }, { "D", 1 }, + { "Li", 3 }, { "Be", 4 }, { "B", 5 }, { "C", 6 }, { "N", 7 }, { "O", 8 }, + { "F", 9 }, { "Na", 11 }, { "Mg", 12 }, { "Al", 13 }, { "Si", 14 }, + { "P", 15 }, { "S", 16 }, { "Cl", 17 }, { "K", 19 }, { "Ca", 20 }, + { "Cr", 24 }, { "Mn", 25 }, { "Fe", 26 }, { "Co", 27 }, { "Ni", 28 }, + { "Cu", 29 }, { "Zn", 30 }, { "Ga", 31 }, { "Ge", 32 }, { "Br", 35 }, + { "La", 57 }, { "Au", 79 } }; int Ions::num_ions_ = -1; short Ions::max_num_proj_ = -1; @@ -700,13 +700,12 @@ void Ions::readLockedAtomNames(HDFrestart& h5f_file) if (dim == 0) return; std::vector data; - h5f_file.readLockedAtomNames(data); + std::string datasetname("/LockedAtomsNames"); + h5f_file.readAtomicData(datasetname, data); - for (std::vector::const_iterator i = data.begin(), - end = data.end(); - i != end; ++i) + for (auto& i : data) { - lockAtom(*i); + lockAtom(i); } } @@ -874,13 +873,17 @@ void Ions::initFromRestartFile(HDFrestart& h5_file) setupListIonsBoundaries(rmax); std::vector at_numbers; - h5_file.readAtomicNumbers(at_numbers); + std::string datasetname("/Atomic_numbers"); + h5_file.readAtomicData(datasetname, at_numbers); std::vector at_indexes; - int nidxs = h5_file.readAtomicIDs(at_indexes); + std::string datasetname_indexes("/Atomic_IDs"); + int nidxs = h5_file.readAtomicData(datasetname_indexes, at_indexes); std::vector at_nlprojIds; - int npids = h5_file.readAtomicNLprojIDs(at_nlprojIds); + std::string datasetname_nlprojIds("/AtomicNLproj_IDs"); + int npids = h5_file.readAtomicData(datasetname_nlprojIds, at_nlprojIds); std::vector at_names; - h5_file.readAtomicNames(at_names); + std::string datasetname_names("/Atomic_names"); + h5_file.readAtomicData(datasetname_names, at_names); if (onpe0 && ct.verbose > 2) { std::cout << "HDF file: at nb=" << at_numbers.size() << std::endl; @@ -908,8 +911,10 @@ void Ions::initFromRestartFile(HDFrestart& h5_file) assert(at_numbers.size() == at_nlprojIds.size()); num_ions_ = at_names.size(); - mmpi.allreduce(&num_ions_, 1, MPI_SUM); - + if (!h5_file.useHdf5p()) + { + mmpi.allreduce(&num_ions_, 1, MPI_SUM); + } if (onpe0 && ct.verbose > 0) { (*MPIdata::sout) << "Ions::setFromRestartFile(), read " << num_ions_ @@ -944,9 +949,21 @@ void Ions::initFromRestartFile(HDFrestart& h5_file) } readRestartPositions(h5_file); readRestartVelocities(h5_file); - readRestartRandomStates(h5_file); + if (ct.LangevinThermostat()) readRestartRandomStates(h5_file); readLockedAtomNames(h5_file); + // remove atoms from local list if not local + for (std::vector::iterator it = local_ions_.begin(); + it != local_ions_.end();) + { + double p[3]; + (*it)->getPosition(p); + if (!inLocalIons(p[0], p[1], p[2])) + it = local_ions_.erase(it); + else + ++it; + } + // rescale all velocities by factor specified in input rescaleVelocities(ct.VelocityScalingFactor()); @@ -967,7 +984,8 @@ void Ions::readRestartPositions(HDFrestart& h5_file) (*MPIdata::sout) << "Read ionic positions from hdf5 file" << std::endl; std::vector data; - h5_file.readAtomicPositions(data); + std::string datasetname("/Ionic_positions"); + h5_file.readAtomicData(datasetname, data); int i = 0; for (auto& ion : local_ions_) @@ -1142,7 +1160,8 @@ void Ions::readRestartVelocities(HDFrestart& h5_file) << std::endl; std::vector data; - h5_file.readAtomicVelocities(data); + std::string datasetname("/Ionic_velocities"); + h5_file.readAtomicData(datasetname, data); int i = 0; for (auto& ion : local_ions_) @@ -1608,7 +1627,6 @@ int Ions::readAtomsFromXYZ( const std::string& filename, const bool cell_relative) { MGmol_MPI& mmpi(*(MGmol_MPI::instance())); - Control& ct(*(Control::instance())); // set up list boundaries // get radius of projectors @@ -1698,9 +1716,6 @@ int Ions::readAtomsFromXYZ( int Ions::setAtoms( const std::vector& crds, const std::vector& spec) { - MGmol_MPI& mmpi(*(MGmol_MPI::instance())); - Control& ct(*(Control::instance())); - const int natoms = crds.size() / 3; double velocity[3] = { 0., 0., 0. }; @@ -1748,8 +1763,6 @@ int Ions::setAtoms( addIonToList(species_[isp], aname, &crds[3 * ia], velocity, locked); } - // std::cout< gids_map; for (unsigned int i = 0; i < gids.size(); i++) diff --git a/src/MD_IonicStepper.cc b/src/MD_IonicStepper.cc index 7e797602..a1b4acb1 100644 --- a/src/MD_IonicStepper.cc +++ b/src/MD_IonicStepper.cc @@ -114,7 +114,8 @@ int MD_IonicStepper::init(HDFrestart& /*h5f_file*/) (*MPIdata::sout) << "MD_IonicStepper::init() --- use positions " "from restart file with dt=" << dt_ << endl; - // taum_: velocities -> displacements = -dt*vel + // taum_ was initialized with velocities + // set taum_ to displacements = -dt*vel double alpha = -1. * dt_; DSCAL(&size_tau, &alpha, &taum_[0], &ione); @@ -123,117 +124,13 @@ int MD_IonicStepper::init(HDFrestart& /*h5f_file*/) taup_ = tau0_; DAXPY(&size_tau, &minus_one, &taum_[0], &ione, &taup_[0], &ione); - // taum_ -> previous positions: tau0_ - dt*vel + // Now set taum_ to previous positions: tau0_ - dt*vel DAXPY(&size_tau, &one, &tau0_[0], &ione, &taum_[0], &ione); } return 0; } -int MD_IonicStepper::writeForces(HDFrestart& h5f_file) -{ - hid_t file_id = h5f_file.file_id(); - - // Create the data space for new datasets - hsize_t dims[2] = { (hsize_t)tau0_.size() / 3, 3 }; - - hid_t dataspace_id = H5Screate_simple(2, dims, nullptr); - if (dataspace_id < 0) - { - (*MPIdata::serr) << "MD_IonicStepper: H5Screate_simple failed!!!" - << endl; - return -1; - } - - // Open dataset - hid_t dataset_id = H5Dcreate2(file_id, "/Ionic_forces", H5T_NATIVE_DOUBLE, - dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); - if (dataset_id < 0) - { - (*MPIdata::serr) - << "MD_IonicStepper::H5Dcreate2 /Ionic_forces failed!!!" << endl; - return -1; - } - - // Write forces - herr_t status = H5Dwrite(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, - H5P_DEFAULT, &fion_[0]); - if (status < 0) - { - (*MPIdata::serr) << "MD_IonicStepper::H5Dwrite forces failed!!!" - << endl; - return -1; - } - else - { - if (onpe0) - (*MPIdata::sout) - << "Ionic forces written into " << h5f_file.filename() << endl; - } - - status = H5Dclose(dataset_id); - if (status < 0) - { - (*MPIdata::serr) << "H5Dclose failed!!!" << endl; - return -1; - } - H5Sclose(dataspace_id); - - return 0; -} - -int MD_IonicStepper::writeTaum(HDFrestart& h5f_file) -{ - hid_t file_id = h5f_file.file_id(); - - // Create the data space for new datasets - hsize_t dims[2] = { (hsize_t)taum_.size() / 3, 3 }; - - hid_t dataspace_id = H5Screate_simple(2, dims, nullptr); - if (dataspace_id < 0) - { - (*MPIdata::serr) << "MD_IonicStepper: H5Screate_simple failed!!!" - << endl; - return -1; - } - - // Open dataset - hid_t dataset_id = H5Dcreate2(file_id, "/Ionic_velocities", - H5T_NATIVE_DOUBLE, dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); - if (dataset_id < 0) - { - (*MPIdata::serr) - << "MD_IonicStepper::H5Dcreate2 /Ionic_velocities failed!!!" - << endl; - return -1; - } - - // Write forces - herr_t status = H5Dwrite(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, - H5P_DEFAULT, &taum_[0]); - if (status < 0) - { - (*MPIdata::serr) << "MD_IonicStepper::H5Dwrite taum failed!!!" << endl; - return -1; - } - else - { - if (onpe0) - (*MPIdata::sout) << "Ionic velocities written into " - << h5f_file.filename() << endl; - } - - status = H5Dclose(dataset_id); - if (status < 0) - { - (*MPIdata::serr) << "H5Dclose failed!!!" << endl; - return -1; - } - H5Sclose(dataspace_id); - - return 0; -} - int MD_IonicStepper::write_hdf5(HDFrestart& h5f_file) { hid_t file_id = h5f_file.file_id(); @@ -251,11 +148,18 @@ int MD_IonicStepper::write_hdf5(HDFrestart& h5f_file) if (status < 0) return status; if (dt_ > 0.) + { writeVelocities(h5f_file); + std::string datasetname("/Ionic_previous_positions"); + writeAtomicFields(h5f_file, taum_, datasetname, true); + } else - writeTaum(h5f_file); - - writeForces(h5f_file); + { + std::string datasetname("/Ionic_velocities"); + writeAtomicFields(h5f_file, taum_, datasetname, true); + } + std::string datasetname("/Ionic_forces"); + writeAtomicFields(h5f_file, fion_, datasetname, true); } // @@ -469,7 +373,8 @@ void MD_IonicStepper::updateTau() tau0_ = taup_; if (dt_ > 0.) { - // update taup to be able to compute velocity... + // update taup_ to be able to compute velocity: + // taup_ <- tau0_-taum_ int size_tau = (int)tau0_.size(); int ione = 1; double alpha = 1.; diff --git a/src/MD_IonicStepper.h b/src/MD_IonicStepper.h index c62b57a5..24705a1a 100644 --- a/src/MD_IonicStepper.h +++ b/src/MD_IonicStepper.h @@ -7,15 +7,8 @@ // This file is part of MGmol. For details, see https://github.com/llnl/mgmol. // Please also read this link https://github.com/llnl/mgmol/LICENSE -//////////////////////////////////////////////////////////////////////////////// -// -// MD_IonicStepper.h: -// -//////////////////////////////////////////////////////////////////////////////// -// $Id$ - -#ifndef MD_IONICSTEPPER_H -#define MD_IONICSTEPPER_H +#ifndef MGMOL_MD_IONICSTEPPER_H +#define MGMOL_MD_IONICSTEPPER_H #include "IonicStepper.h" #include @@ -72,8 +65,6 @@ class MD_IonicStepper : public IonicStepper void updateTau(); double etol(void) const override; int write_hdf5(HDFrestart&) override; - int writeForces(HDFrestart& h5f_file); - int writeTaum(HDFrestart& h5f_file); int init(HDFrestart&) override; void printVelocities(std::ostream& os) const; diff --git a/src/MVP_DMStrategy.h b/src/MVP_DMStrategy.h index 4b7e3be0..2c16fbcc 100644 --- a/src/MVP_DMStrategy.h +++ b/src/MVP_DMStrategy.h @@ -48,7 +48,7 @@ class MVP_DMStrategy : public DMStrategy const std::vector>& overlappingGids, ProjectedMatricesInterface* proj_matrices, const bool use_old_dm); - void initialize(OrbitalsType& orbitals) override{}; + void initialize(OrbitalsType&) override{}; int update(OrbitalsType& orbitals) override; // H is updated with MVP loop, so no need to compute it outside diff --git a/src/Potentials.cc b/src/Potentials.cc index a54f0c47..9916c021 100644 --- a/src/Potentials.cc +++ b/src/Potentials.cc @@ -37,9 +37,8 @@ Potentials::~Potentials() #endif } -Potentials::Potentials(const bool vh_frozen) +Potentials::Potentials() { - //(*MPIdata::sout)<<"Potentials::setup()"<::MPaxpy(size_, alpha, &v_comp_[0], v); } +void Potentials::backupVh() +{ + memcpy(vh_rho_backup_.data(), vh_rho_.data(), size_ * sizeof(POTDTYPE)); +} + void Potentials::initializeSupersampledRadialDataOnMesh( const Vector3D& position, const Species& sp) { diff --git a/src/Potentials.h b/src/Potentials.h index 0ddd10fa..f0f762b3 100644 --- a/src/Potentials.h +++ b/src/Potentials.h @@ -76,6 +76,11 @@ class Potentials std::vector dv_; + /*! + * Backpup copy of Hartree potential to save previous state + */ + std::vector vh_rho_backup_; + int itindex_vxc_; int itindex_vh_; @@ -99,7 +104,7 @@ class Potentials const Vector3D& position, const Species& sp, const std::vector &local_idx, std::vector &sampled_rhoc); public: - Potentials(const bool vh_frozen = false); + Potentials(); ~Potentials(); @@ -141,14 +146,15 @@ class Potentials double scf_dvrho(void) const { return scf_dvrho_; } double scf_dv(void) const { return scf_dv_; } - POTDTYPE* vtot() { return &vtot_[0]; } - POTDTYPE* vh_rho() { return &vh_rho_[0]; } - RHODTYPE* rho_comp() { return &rho_comp_[0]; } + POTDTYPE* vtot() { return vtot_.data(); } + POTDTYPE* vh_rho() { return vh_rho_.data(); } + RHODTYPE* rho_comp() { return rho_comp_.data(); } const std::vector& vnuc() const { return v_nuc_; } - POTDTYPE* vnuc() { return &v_nuc_[0]; } - POTDTYPE* vext() { return &v_ext_[0]; } - POTDTYPE* vepsilon() { return &vepsilon_[0]; } + POTDTYPE* vnuc() { return v_nuc_.data(); } + POTDTYPE* vext() { return v_ext_.data(); } + POTDTYPE* vepsilon() { return vepsilon_.data(); } + POTDTYPE* vh_rho_backup() { return vh_rho_backup_.data(); } void axpVcompToVh(const double alpha); void axpVcomp(POTDTYPE* v, const double alpha); @@ -162,8 +168,6 @@ class Potentials double getChargeInCell() const { return charge_in_cell_; } - const double getBackgroundCharge() const { return background_charge_; } - /*! * initialize total potential as local pseudopotential */ @@ -201,6 +205,11 @@ class Potentials void initBackground(Ions& ions); void addBackgroundToRhoComp(); + /*! + * Save current Hartree potential into backup array + */ + void backupVh(); + void evalIonDensityOnSamplePts(Ions& ions, const std::vector &local_idx, std::vector &sampled_rhoc); #ifdef HAVE_TRICUBIC diff --git a/src/hdf_tools.cc b/src/hdf_tools.cc index e56c0478..d0308875 100644 --- a/src/hdf_tools.cc +++ b/src/hdf_tools.cc @@ -22,6 +22,18 @@ namespace mgmol_tools { +void string2fixedlength( + std::vector& data, std::vector& tc) +{ + tc.clear(); + for (auto& d : data) + { + FixedLengthString t; + strncpy(t.mystring, d.c_str(), IonData_MaxStrLength - 1); + tc.push_back(t); + } +} + void write1d(hid_t file_id, const std::string& datasetname, std::vector& data, size_t length) { @@ -235,14 +247,7 @@ void write2d(hid_t file_id, const std::string& datasetname, // First copy the contents of the vector into a temporary container std::vector tc; - for (std::vector::const_iterator i = data.begin(), - end = data.end(); - i != end; ++i) - { - FixedLengthString t; - strncpy(t.mystring, i->c_str(), IonData_MaxStrLength); - tc.push_back(t); - } + string2fixedlength(data, tc); std::string attname("String_Length"); hsize_t dimsA[1] = { 1 }; @@ -583,14 +588,7 @@ void parallelWrite2d(hid_t file_id, const std::string& datasetname, // First copy the contents of the vector into a temporary container std::vector tc; - for (std::vector::const_iterator i = data.begin(), - end = data.end(); - i != end; ++i) - { - FixedLengthString t; - strncpy(t.mystring, i->c_str(), IonData_MaxStrLength); - tc.push_back(t); - } + string2fixedlength(data, tc); status = H5Dwrite(dset_id, strtype, memspace, filespace, plist_id, &tc[0]); if (status < 0) { diff --git a/src/md.cc b/src/md.cc index 01e34a87..1d5ee937 100644 --- a/src/md.cc +++ b/src/md.cc @@ -54,6 +54,9 @@ void MGmol::moveVnuc(Ions& ions) Potentials& pot = hamiltonian_->potential(); + // save Hartree potential internally + pot.backupVh(); + // Update items that change when the ionic coordinates change pot.axpVcompToVh(1.); initNuc(ions); diff --git a/src/mgmol_run.cc b/src/mgmol_run.cc index e746611c..a5de1ad5 100644 --- a/src/mgmol_run.cc +++ b/src/mgmol_run.cc @@ -91,7 +91,6 @@ int mgmol_check() Control& ct = *(Control::instance()); Mesh* mymesh = Mesh::instance(); const pb::PEenv& myPEenv = mymesh->peenv(); - MGmol_MPI& mmpi = *(MGmol_MPI::instance()); if (myPEenv.color() > 0) { diff --git a/src/restart.cc b/src/restart.cc index 2fa76ecb..30bdad73 100644 --- a/src/restart.cc +++ b/src/restart.cc @@ -117,7 +117,7 @@ int MGmol::write_hdf5(HDFrestart& h5f_file, ions.writeAtomicIDs(h5f_file); ions.writeAtomicNLprojIDs(h5f_file); ions.writePositions(h5f_file); - ions.writeRandomStates(h5f_file); + if (ct.LangevinThermostat()) ions.writeRandomStates(h5f_file); ions.writeVelocities(h5f_file); ions.writeForces(h5f_file); @@ -141,6 +141,14 @@ int MGmol::write_hdf5(HDFrestart& h5f_file, pot.vh_rho(), "Hartree", &ll[0], &origin[0]); if (ierr < 0) return ierr; + if (ct.AtomsDynamic() == AtomsDynamicType::MD) + { + // Write hartree potential before extrapolation + ierr = h5f_file.write_1func_hdf5( + pot.vh_rho_backup(), "Preceding_Hartree", &ll[0], &origin[0]); + if (ierr < 0) return ierr; + } + // Write if (ct.diel) { diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt index 1855eb1e..6b5514d2 100644 --- a/tests/CMakeLists.txt +++ b/tests/CMakeLists.txt @@ -514,6 +514,14 @@ add_test(NAME testMD_D72 ${CMAKE_CURRENT_SOURCE_DIR}/MD_D72/coords.in ${CMAKE_CURRENT_SOURCE_DIR}/MD_D72/lrs.in ${CMAKE_CURRENT_SOURCE_DIR}/../potentials) +add_test(NAME testHDF5single + COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/HDF5single/test.py + ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} 4 ${MPIEXEC_PREFLAGS} + ${CMAKE_CURRENT_BINARY_DIR}/../src/mgmol-opt + ${CMAKE_CURRENT_SOURCE_DIR}/HDF5single/mgmol.cfg + ${CMAKE_CURRENT_SOURCE_DIR}/HDF5single/md.cfg + ${CMAKE_CURRENT_SOURCE_DIR}/HDF5single/h2o.xyz + ${CMAKE_CURRENT_SOURCE_DIR}/../potentials) add_test(NAME testMD_MVP COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/MD_MVP/test.py ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} 4 ${MPIEXEC_PREFLAGS} diff --git a/tests/DMandEnergyAndForces/test.py b/tests/DMandEnergyAndForces/test.py index c36f0767..b21e6e72 100755 --- a/tests/DMandEnergyAndForces/test.py +++ b/tests/DMandEnergyAndForces/test.py @@ -3,6 +3,7 @@ import os import subprocess import string +import shutil print("Test DMandEnergyAndForces...") @@ -33,6 +34,8 @@ output = subprocess.check_output(command,shell=True) lines=output.split(b'\n') +shutil.rmtree('WF') + #analyse output energies=[] for line in lines: diff --git a/tests/HDF5single/h2o.xyz b/tests/HDF5single/h2o.xyz new file mode 100644 index 00000000..d5171c8b --- /dev/null +++ b/tests/HDF5single/h2o.xyz @@ -0,0 +1,6 @@ +3 + +O 0.00 0.00 0.00 +H -0.76 0.59 0.00 +H 0.76 0.59 0.00 + diff --git a/tests/HDF5single/md.cfg b/tests/HDF5single/md.cfg new file mode 100644 index 00000000..1ff2adab --- /dev/null +++ b/tests/HDF5single/md.cfg @@ -0,0 +1,34 @@ +verbosity=3 +xcFunctional=PBE +FDtype=4th +[Mesh] +nx=48 +ny=48 +nz=48 +[Domain] +ox=-4.5 +oy=-4.5 +oz=-4.5 +lx=9. +ly=9. +lz=9. +[Potentials] +pseudopotential=pseudo.O_ONCV_PBE_SG15 +pseudopotential=pseudo.H_ONCV_PBE_SG15 +[Run] +type=MD +[MD] +num_steps=5 +dt=40. +[Quench] +max_steps=24 +atol=1.e-8 +[Restart] +input_level=4 +input_filename=WF +input_type=single_file +output_level=4 +output_filename=WF_MD +output_type=single_file +[Coloring] +scope=global diff --git a/tests/HDF5single/mgmol.cfg b/tests/HDF5single/mgmol.cfg new file mode 100644 index 00000000..4dba942a --- /dev/null +++ b/tests/HDF5single/mgmol.cfg @@ -0,0 +1,31 @@ +verbosity=2 +xcFunctional=PBE +FDtype=4th +[Mesh] +nx=48 +ny=48 +nz=48 +[Domain] +ox=-4.5 +oy=-4.5 +oz=-4.5 +lx=9. +ly=9. +lz=9. +[Potentials] +pseudopotential=pseudo.O_ONCV_PBE_SG15 +pseudopotential=pseudo.H_ONCV_PBE_SG15 +[Run] +type=QUENCH +[Quench] +max_steps=120 +atol=1.e-8 +[Orbitals] +initial_type=Random +initial_width=1.5 +[Restart] +output_level=4 +output_filename=WF +output_type=single_file +[Coloring] +scope=global diff --git a/tests/HDF5single/test.py b/tests/HDF5single/test.py new file mode 100755 index 00000000..080ee0ba --- /dev/null +++ b/tests/HDF5single/test.py @@ -0,0 +1,75 @@ +#!/usr/bin/env python +import sys +import os +import subprocess +import string + +print("Test test_rho_restart...") + +nargs=len(sys.argv) + +mpicmd = sys.argv[1]+" "+sys.argv[2]+" "+sys.argv[3] +for i in range(4,nargs-7): + mpicmd = mpicmd + " "+sys.argv[i] +print("MPI run command: {}".format(mpicmd)) + +mgmol_exe = sys.argv[nargs-5] +input1 = sys.argv[nargs-4] +input2 = sys.argv[nargs-3] +coords = sys.argv[nargs-2] +print("coordinates file: %s"%coords) + +#create links to potentials files +dst1 = 'pseudo.H_ONCV_PBE_SG15' +src1 = sys.argv[-1] + '/' + dst1 + +dst2 = 'pseudo.O_ONCV_PBE_SG15' +src2 = sys.argv[-1] + '/' + dst2 + +if not os.path.exists(dst1): + print("Create link to %s"%dst1) + os.symlink(src1, dst1) + +if not os.path.exists(dst2): + print("Create link to %s"%dst2) + os.symlink(src2, dst2) + +#run mgmol to generate initial ground state +command = "{} {} -c {} -i {}".format(mpicmd,mgmol_exe,input1,coords) +print("Run command: {}".format(command)) + +output = subprocess.check_output(command,shell=True) +lines=output.split(b'\n') + +#run MD +command = "{} {} -c {} -i {}".format(mpicmd,mgmol_exe,input2,coords) +print("Run command: {}".format(command)) +output = subprocess.check_output(command,shell=True) +lines=output.split(b'\n') + +os.remove('WF') + +print("Check energy conservation...") +tol = 1.e-4 +energy = 0. +count = 0 +for line in lines: + if line.count(b'Total') and line.count(b'Energy'): + print(line) + count=count+1 + words=line.split() + + energy=eval(words[2]) + if count==1: + first_energy=energy + + if count>1 and abs(energy-first_energy)>tol: + print("ERROR Energy = {} != {}".format(energy,first_energy)) + sys.exit(1) + +if count<4: + print("ERROR needs 4 energy values for checking conservation!") + sys.exit(1) + +print("Test SUCCESSFUL!") +sys.exit(0) diff --git a/tests/RestartEnergyAndForces/test.py b/tests/RestartEnergyAndForces/test.py index 349434e8..b62d39f8 100755 --- a/tests/RestartEnergyAndForces/test.py +++ b/tests/RestartEnergyAndForces/test.py @@ -3,6 +3,7 @@ import os import subprocess import string +import shutil print("Test RestartEnergyAndForces...") @@ -54,14 +55,14 @@ ref_energy=energy break -#sys.exit(0) - #run test command = "{} {} -c {} -i {}".format(mpicmd,test_exe,input2,coords) print("Run command: {}".format(command)) output = subprocess.check_output(command,shell=True) lines=output.split(b'\n') +shutil.rmtree('WF') + test_energy=1.e18 for line in lines: if line.count(b'%%'): diff --git a/tests/WFEnergyAndForces/test.py b/tests/WFEnergyAndForces/test.py index 45420ddf..6cac8c93 100755 --- a/tests/WFEnergyAndForces/test.py +++ b/tests/WFEnergyAndForces/test.py @@ -3,6 +3,7 @@ import os import subprocess import string +import shutil print("Test WFEnergyAndForces...") @@ -37,6 +38,8 @@ output = subprocess.check_output(command,shell=True) lines=output.split(b'\n') +shutil.rmtree('WF') + #analyse output energies=[] for line in lines: diff --git a/tests/testSetGhostValues.cc b/tests/testSetGhostValues.cc index f8520055..c3680087 100644 --- a/tests/testSetGhostValues.cc +++ b/tests/testSetGhostValues.cc @@ -18,8 +18,6 @@ TEST_CASE("Set ghost values", "[set ghosts") const double ll = 1.; const double lattice[3] = { ll, ll, ll }; - const int nfunc = 10; - MGmol_MPI::setup(MPI_COMM_WORLD, std::cout); MGmol_MPI& mmpi = *(MGmol_MPI::instance()); @@ -101,8 +99,6 @@ TEST_CASE("Set ghost values", "[set ghosts") gf.assign(inner_data.data(), 'd'); gf.set_updated_boundaries(false); - double norm_before = gf.norm2(); - // fill ghost values const bool direction[3] = { true, true, true }; gf.defaultTrade_boundaries();