diff --git a/parser/parser-cpmd/cpmdparser/parser.py b/parser/parser-cpmd/cpmdparser/parser.py index e1c0ab2c7768276c575f2f6aebbc1efd3f33ce81..114a3a3f71119b112ba1f9ed9b705a62bb351b31 100644 --- a/parser/parser-cpmd/cpmdparser/parser.py +++ b/parser/parser-cpmd/cpmdparser/parser.py @@ -37,6 +37,7 @@ class CPMDParser(ParserInterface): regex_version = re.compile("\s+VERSION ([\d\.]+)") regex_single_point = re.compile(r" SINGLE POINT DENSITY OPTIMIZATION") regex_geo_opt = re.compile(r" OPTIMIZATION OF IONIC POSITIONS") + regex_md = re.compile(r" CAR-PARRINELLO MOLECULAR DYNAMICS") run_type = None n_lines = 1000 version_id = None @@ -62,6 +63,11 @@ class CPMDParser(ParserInterface): if result_single_point: run_type = CPMDRunType(module_name="singlepointparser", class_name="CPMDSinglePointParser") + # Look for MD calculation + result_md = regex_md.match(line) + if result_md: + run_type = CPMDRunType(module_name="mdparser", class_name="CPMDMDParser") + if version_id is None: msg = "Could not find a version specification from the given main file." logger.exception(msg) diff --git a/parser/parser-cpmd/cpmdparser/versions/cpmd41/commonparser.py b/parser/parser-cpmd/cpmdparser/versions/cpmd41/commonparser.py index 154ecf80cb54333561abef4d6c3d04ca20f8e3fe..21e040962fa5c25ef37dfcc462b9c6acde989704 100644 --- a/parser/parser-cpmd/cpmdparser/versions/cpmd41/commonparser.py +++ b/parser/parser-cpmd/cpmdparser/versions/cpmd41/commonparser.py @@ -25,6 +25,8 @@ class CPMDCommonParser(CommonParser): self.cache_service.add("atom_labels", single=False, update=False) self.cache_service.add("number_of_atoms", single=False, update=False) self.cache_service.add("simulation_cell", single=False, update=False) + self.cache_service.add("n_steps") + self.cache_service.add("ensemble_type") #=========================================================================== # Common SimpleMatchers @@ -50,7 +52,7 @@ class CPMDCommonParser(CommonParser): """Returns the simplematcher that parses informatio about the method used. Common to all run types. """ - return SM( "(?: SINGLE POINT DENSITY OPTIMIZATION)|(?: OPTIMIZATION OF IONIC POSITIONS)", + return SM( "(?: SINGLE POINT DENSITY OPTIMIZATION)|(?: OPTIMIZATION OF IONIC POSITIONS)|(?: CAR-PARRINELLO MOLECULAR DYNAMICS)", subMatchers=[ SM( " USING SEED", forwardMatch=True, @@ -59,7 +61,13 @@ class CPMDCommonParser(CommonParser): SM( " USING SEED\s+{}\s+TO INIT. PSEUDO RANDOM NUMBER GEN.".format(self.regexs.int)), SM( " PATH TO THE RESTART FILES:\s+{}".format(self.regexs.eol)), SM( " GRAM-SCHMIDT ORTHOGONALIZATION"), - SM( " MAXIMUM NUMBER OF STEPS:\s+{} STEPS".format(self.regexs.int)), + SM( " ITERATIVE ORTHOGONALIZATION", + subMatchers={ + SM(" MAXIT:\s+{}".format(self.regexs.int)), + SM(" EPS:\s+{}".format(self.regexs.float)), + } + ), + SM( " MAXIMUM NUMBER OF STEPS:\s+(?P<x_cpmd_max_steps>{}) STEPS".format(self.regexs.int)), SM( " MAXIMUM NUMBER OF ITERATIONS FOR SC:\s+(?P<scf_max_iteration>{}) STEPS".format(self.regexs.int)), SM( " PRINT INTERMEDIATE RESULTS EVERY\s+{} STEPS".format(self.regexs.int)), SM( " STORE INTERMEDIATE RESULTS EVERY\s+{} STEPS".format(self.regexs.int)), @@ -69,6 +77,12 @@ class CPMDCommonParser(CommonParser): SM( " FICTITIOUS ELECTRON MASS:\s+{}".format(self.regexs.float)), SM( " TIME STEP FOR ELECTRONS:\s+{}".format(self.regexs.float)), SM( " TIME STEP FOR IONS:\s+{}".format(self.regexs.float)), + + SM( " TRAJECTORIES ARE SAVED ON FILE"), + SM( " TRAJEC\.xyz IS SAVED ON FILE"), + SM( " ELECTRON DYNAMICS:"), + SM( " ION DYNAMICS:(?P<x_cpmd_ion_temperature_control>{})".format(self.regexs.eol)), + SM( " CONVERGENCE CRITERIA FOR WAVEFUNCTION OPTIMIZATION:\s+(?P<scf_threshold_energy_change__hartree>{})".format(self.regexs.float)), SM( " WAVEFUNCTION OPTIMIZATION BY PRECONDITIONED DIIS"), SM( " THRESHOLD FOR THE WF-HESSIAN IS\s+{}".format(self.regexs.float)), @@ -259,7 +273,16 @@ class CPMDCommonParser(CommonParser): } geo_opt_method = geo_opt_method_mapping.get(geo_opt_method) if geo_opt_method is not None: - backend.addValue("geometry_optimization_method", "bfgs") + backend.addValue("geometry_optimization_method", geo_opt_method) + + # Number of steps + n_steps = section.get_latest_value("x_cpmd_max_steps") + self.cache_service["n_steps"] = n_steps + + # Temperature control for ions + temp_control = section.get_latest_value("x_cpmd_ion_temperature_control") + if temp_control.strip() == "THE TEMPERATURE IS NOT CONTROLLED": + self.cache_service["ensemble_type"] = "NVE" #=========================================================================== # adHoc functions diff --git a/parser/parser-cpmd/cpmdparser/versions/cpmd41/geooptparser.py b/parser/parser-cpmd/cpmdparser/versions/cpmd41/geooptparser.py index 546e4fa7bee761cb66a73563dbe8dc7b0cda2b75..31265fa605dc117373e47020faa2bcd821e6357f 100644 --- a/parser/parser-cpmd/cpmdparser/versions/cpmd41/geooptparser.py +++ b/parser/parser-cpmd/cpmdparser/versions/cpmd41/geooptparser.py @@ -1,8 +1,6 @@ from __future__ import absolute_import from nomadcore.simple_parser import SimpleMatcher as SM from nomadcore.baseclasses import MainHierarchicalParser -# from nomadcore.unit_conversion.unit_conversion import convert_unit -# from nomadcore.caching_backend import CachingLevel import numpy as np from .commonparser import CPMDCommonParser import re diff --git a/parser/parser-cpmd/cpmdparser/versions/cpmd41/mdparser.py b/parser/parser-cpmd/cpmdparser/versions/cpmd41/mdparser.py new file mode 100644 index 0000000000000000000000000000000000000000..956e32b7c2410ea97838e5822968bfb7f0e37a5e --- /dev/null +++ b/parser/parser-cpmd/cpmdparser/versions/cpmd41/mdparser.py @@ -0,0 +1,159 @@ +from __future__ import absolute_import +import re +import logging +import numpy as np +from .commonparser import CPMDCommonParser +from nomadcore.simple_parser import SimpleMatcher as SM +from nomadcore.baseclasses import MainHierarchicalParser +import nomadcore.csvparsing +import nomadcore.configurationreading +LOGGER = logging.getLogger("nomad") + + +#=============================================================================== +class CPMDMDParser(MainHierarchicalParser): + """The main parser class that is called for all run types. Parses the CPMD + output file. + """ + def __init__(self, file_path, parser_context): + """ + """ + super(CPMDMDParser, self).__init__(file_path, parser_context) + self.setup_common_matcher(CPMDCommonParser(parser_context)) + self.sampling_method_gid = None + self.frame_refs = [] + self.energies = [] + + # Detect what files are available in the same folder where the main + # file is located. + self.dcd_filepath = self.file_service.get_absolute_path_to_file("TRAJEC.dcd") + self.xyz_filepath = self.file_service.get_absolute_path_to_file("TRAJEC.xyz") + self.trajectory_filepath = self.file_service.get_absolute_path_to_file("TRAJECTORY") + self.ftrajectory_filepath = self.file_service.get_absolute_path_to_file("FTRAJECTORY") + + #======================================================================= + # Cache levels + # self.caching_levels.update({ + # 'section_run': CachingLevel.ForwardAndCache, + # }) + + #======================================================================= + # Main structure + self.root_matcher = SM("", + forwardMatch=True, + sections=['section_run', "section_frame_sequence", "section_sampling_method", "section_method"], + subMatchers=[ + self.cm.header(), + self.cm.method(), + self.cm.atoms(), + self.cm.cell(), + self.cm.initialization(), + SM( " DEGREES OF FREEDOM FOR SYSTEM:", + sections=["x_cpmd_section_md_initialization"], + forwardMatch=True, + subMatchers=[ + SM( " DEGREES OF FREEDOM FOR SYSTEM:"), + SM( " RVSCAL| RESCALING IONIC TEMP FROM\s+{0} TO\s+{0}".format(self.regexs.float)), + SM( re.escape(" == FORCES INITIALIZATION ==")), + SM( " EWALD\| SUM IN REAL SPACE OVER\s+{0}\*\s+{0}\*\s+{0} CELLS".format(self.regexs.int)), + SM( re.escape(" == END OF FORCES INITIALIZATION ==")), + SM( " TIME FOR INITIALIZATION:\s+{} SECONDS".format(self.regexs.float)), + ] + ), + SM( " NFI EKINC TEMPP EKS ECLASSIC EHAM DIS TCPU", + adHoc=self.ad_hoc_parse_md(), + ), + self.cm.footer(), + ] + ) + + #======================================================================= + # onClose triggers + # def onClose_section_single_configuration_calculation(self, backend, gIndex, section): + # # For single point calculations there is only one method and system. + # backend.addValue("single_configuration_calculation_to_system_ref", 0) + # backend.addValue("single_configuration_to_calculation_method_ref", 0) + # self.frame_refs.append(gIndex) + + # def onClose_section_frame_sequence(self, backend, gIndex, section): + # backend.addValue("number_of_frames_in_sequence", self.n_frames) + # if self.sampling_method_gid is not None: + # backend.addValue("frame_sequence_to_sampling_ref", self.sampling_method_gid) + # if self.frame_refs: + # backend.addArrayValues("frame_sequence_local_frames_ref", np.array(self.frame_refs)) + # if self.energies: + # backend.addArrayValues("frame_sequence_potential_energy", np.array(self.energies)) + + def onClose_section_sampling_method(self, backend, gIndex, section): + self.sampling_method_gid = gIndex + backend.addValue("sampling_method", "molecular_dynamics") + self.cache_service.addValue("ensemble_type") + + # def onClose_section_system(self, backend, gIndex, section): + # self.cache_service.addArrayValues("atom_labels") + # self.cache_service.addArrayValues("simulation_cell", unit="bohr") + # self.cache_service.addValue("number_of_atoms") + + #======================================================================= + # adHoc + def ad_hoc_parse_md(self): + """Parses all the md step information. + """ + def wrapper(parser): + + # Decide from which file trajectory is read + traj_file = None + traj_format = None + traj_step = 1 + traj_iterator = None + traj_unit = None + if self.dcd_filepath: + traj_file = self.dcd_filepath + traj_format = "dcd" + traj_unit = "angstrom" + elif self.xyz_filepath: + traj_file = self.xyz_filepath + traj_format = "xyz" + traj_unit = "angstrom" + elif self.trajectory_filepath: + traj_file = self.trajectory_filepath + traj_format = "custom" + traj_unit = "bohr" + + # Initialize the trajectory iterator + if traj_format == "custom": + n_atoms = self.cache_service["number_of_atoms"] + traj_iterator = nomadcore.csvparsing.iread(traj_file, columns=[1, 2, 3], n_conf=n_atoms) + else: + try: + traj_iterator = nomadcore.configurationreading.iread(traj_file) + except ValueError: + pass + + # Start reading the frames + i_frame = 0 + n_frames = self.cache_service["n_steps"] + parser.backend.addValue("number_of_frames_in_sequence", n_frames) + + for i_frame in range(n_frames): + scc_id = parser.backend.openSection("section_single_configuration_calculation") + sys_id = parser.backend.openSection("section_system") + + # System + self.cache_service.addArrayValues("atom_labels") + self.cache_service.addArrayValues("simulation_cell", unit="bohr") + self.cache_service.addValue("number_of_atoms") + + # Coordinates + if i_frame % traj_step == 0: + try: + pos = next(traj_iterator) + except StopIteration: + LOGGER.error("Could not get the next geometries from an external file. It seems that the number of MD steps in the CPMD outputfile doesn't match the number of steps found in the external trajectory file.") + else: + parser.backend.addArrayValues("atom_positions", pos, unit=traj_unit) + + parser.backend.closeSection("section_single_configuration_calculation", scc_id) + parser.backend.closeSection("section_system", sys_id) + + return wrapper diff --git a/src/main/scala/eu/nomad_lab/parsers/CpmdParser.scala b/src/main/scala/eu/nomad_lab/parsers/CpmdParser.scala index d1da8ecd764e47912d5775cea644e304a999d825..217f3ce469c36ede03a1b24874269e33c857b177 100644 --- a/src/main/scala/eu/nomad_lab/parsers/CpmdParser.scala +++ b/src/main/scala/eu/nomad_lab/parsers/CpmdParser.scala @@ -41,6 +41,7 @@ object CpmdParser extends SimpleExternalParserGenerator( "parser-cpmd/cpmdparser/versions/__init__.py", "parser-cpmd/cpmdparser/versions/cpmd41/__init__.py", "parser-cpmd/cpmdparser/versions/cpmd41/geooptparser.py", + "parser-cpmd/cpmdparser/versions/cpmd41/mdparser.py", "parser-cpmd/cpmdparser/versions/cpmd41/singlepointparser.py", "parser-cpmd/cpmdparser/versions/cpmd41/inputparser.py", "parser-cpmd/cpmdparser/versions/cpmd41/commonparser.py", diff --git a/src/test/scala/eu/nomad_lab/parsers/CpmdParserSpec.scala b/src/test/scala/eu/nomad_lab/parsers/CpmdParserSpec.scala index f08a7c5ba9b05fbbc97f385628d4b3d005dac24c..4d965b7b251840980d271b474a51463fdc4abe35 100644 --- a/src/test/scala/eu/nomad_lab/parsers/CpmdParserSpec.scala +++ b/src/test/scala/eu/nomad_lab/parsers/CpmdParserSpec.scala @@ -12,7 +12,10 @@ object CpmdParserSpec extends Specification { "test energy_force with json" >> { ParserRun.parse(CpmdParser, "parsers/cpmd/test/examples/single_point/output.out", "json") must_== ParseResult.ParseSuccess } - "test energy_force with json" >> { + "test geo_opt with json" >> { ParserRun.parse(CpmdParser, "parsers/cpmd/test/examples/geo_opt/output.out", "json") must_== ParseResult.ParseSuccess } + "test md with json" >> { + ParserRun.parse(CpmdParser, "parsers/cpmd/test/examples/md/output.out", "json") must_== ParseResult.ParseSuccess + } } diff --git a/test/examples/md/ENERGIES b/test/examples/md/ENERGIES new file mode 100644 index 0000000000000000000000000000000000000000..3779f299b02fbce5ef6fbb2303f56c6cf2d640e7 --- /dev/null +++ b/test/examples/md/ENERGIES @@ -0,0 +1,50 @@ + 1 0.00472945 110.096 -1.1023492072 -1.1018262261 -1.0970967730 0.288545E-05 0.25 + 2 0.01424065 232.496 -1.1128688938 -1.1117644858 -1.0975238350 0.182162E-04 0.25 + 3 0.02228702 351.956 -1.1216882365 -1.1200163669 -1.0977293448 0.596327E-04 0.25 + 4 0.02592222 412.578 -1.1256188624 -1.1236590243 -1.0977368045 0.137607E-03 0.24 + 5 0.02507375 393.180 -1.1245335482 -1.1226658551 -1.0975921059 0.251896E-03 0.23 + 6 0.02170348 311.439 -1.1206087528 -1.1191293469 -1.0974258636 0.389716E-03 0.24 + 7 0.01806912 208.928 -1.1163887071 -1.1153962539 -1.0973271357 0.530786E-03 0.23 + 8 0.01550309 123.508 -1.1133979574 -1.1128112667 -1.0973081718 0.656212E-03 0.23 + 9 0.01428927 71.351 -1.1119610076 -1.1116220739 -1.0973328023 0.755177E-03 0.24 + 10 0.01412005 48.653 -1.1117171754 -1.1114860650 -1.0973660187 0.826435E-03 0.23 + 11 0.01454963 43.205 -1.1121477411 -1.1119425095 -1.0973928823 0.875667E-03 0.23 + 12 0.01522198 44.147 -1.1128400647 -1.1126303571 -1.0974083755 0.911456E-03 0.23 + 13 0.01592316 45.526 -1.1135548344 -1.1133385763 -1.0974154187 0.942258E-03 0.23 + 14 0.01655033 45.568 -1.1141854503 -1.1139689917 -1.0974186637 0.974901E-03 0.24 + 15 0.01706605 44.715 -1.1146975180 -1.1144851121 -1.0974190627 0.101412E-02 0.23 + 16 0.01746680 44.005 -1.1150947618 -1.1148857283 -1.0974189329 0.106282E-02 0.22 + 17 0.01776074 44.244 -1.1153899632 -1.1151797929 -1.0974190575 0.112264E-02 0.24 + 18 0.01795742 45.772 -1.1155935307 -1.1153761050 -1.0974186815 0.119434E-02 0.23 + 19 0.01806576 48.537 -1.1157147808 -1.1154842182 -1.0974184559 0.127815E-02 0.23 + 20 0.01809373 52.255 -1.1157599169 -1.1155116921 -1.0974179583 0.137401E-02 0.23 + 21 0.01805054 56.516 -1.1157360008 -1.1154675379 -1.0974169961 0.148167E-02 0.23 + 22 0.01794636 60.905 -1.1156512292 -1.1153619159 -1.0974155607 0.160074E-02 0.24 + 23 0.01779314 65.074 -1.1155167676 -1.1152076534 -1.0974145094 0.173073E-02 0.23 + 24 0.01760410 68.722 -1.1153426839 -1.1150162383 -1.0974121397 0.187108E-02 0.24 + 25 0.01739640 71.638 -1.1151469827 -1.1148066858 -1.0974102809 0.202107E-02 0.24 + 26 0.01718921 73.709 -1.1149481806 -1.1145980447 -1.0974088338 0.217994E-02 0.23 + 27 0.01699582 74.870 -1.1147573603 -1.1144017101 -1.0974058862 0.234681E-02 0.23 + 28 0.01683495 75.111 -1.1145981234 -1.1142413309 -1.0974063855 0.252070E-02 0.25 + 29 0.01670265 74.489 -1.1144603569 -1.1141065157 -1.0974038654 0.270054E-02 0.24 + 30 0.01661442 73.081 -1.1143644220 -1.1140172732 -1.0974028537 0.288524E-02 0.24 + 31 0.01655815 70.980 -1.1143033888 -1.1139662190 -1.0974080684 0.307358E-02 0.23 + 32 0.01650569 68.325 -1.1142240908 -1.1138995296 -1.0973938363 0.326432E-02 0.23 + 33 0.01657766 65.255 -1.1142857160 -1.1139757411 -1.0973980782 0.345624E-02 0.23 + 34 0.01674936 61.905 -1.1144438592 -1.1141497957 -1.0974004352 0.364807E-02 0.23 + 35 0.01702316 58.440 -1.1146791594 -1.1144015566 -1.0973784004 0.383857E-02 0.23 + 36 0.01763441 55.015 -1.1152782856 -1.1150169543 -1.0973825424 0.402661E-02 0.23 + 37 0.01848514 51.771 -1.1161573098 -1.1159113844 -1.0974262399 0.421112E-02 0.23 + 38 0.01897016 48.857 -1.1166648547 -1.1164327728 -1.0974626172 0.439118E-02 0.23 + 39 0.01858750 46.386 -1.1162605862 -1.1160402423 -1.0974527395 0.456614E-02 0.22 + 40 0.01744917 44.419 -1.1150750202 -1.1148640199 -1.0974148488 0.473558E-02 0.23 + 41 0.01610603 42.978 -1.1136853843 -1.1134812305 -1.0973752036 0.489928E-02 0.23 + 42 0.01516204 42.048 -1.1127114865 -1.1125117498 -1.0973497053 0.505718E-02 0.23 + 43 0.01497724 41.607 -1.1125324644 -1.1123348215 -1.0973575818 0.520925E-02 0.23 + 44 0.01549914 41.655 -1.1130663421 -1.1128684718 -1.0973693342 0.535541E-02 0.24 + 45 0.01649282 42.196 -1.1140950557 -1.1138946136 -1.0974017920 0.549556E-02 0.24 + 46 0.01752242 43.235 -1.1151502868 -1.1149449129 -1.0974224937 0.562968E-02 0.23 + 47 0.01826876 44.768 -1.1159079382 -1.1156952780 -1.0974265218 0.575782E-02 0.29 + 48 0.01863973 46.745 -1.1162911025 -1.1160690555 -1.0974293221 0.588031E-02 0.28 + 49 0.01862430 49.045 -1.1162747263 -1.1160417513 -1.0974174556 0.599772E-02 0.24 + 50 0.01840782 51.542 -1.1160488582 -1.1158040226 -1.0973962069 0.611084E-02 0.23 diff --git a/test/examples/md/GEOMETRY b/test/examples/md/GEOMETRY new file mode 100644 index 0000000000000000000000000000000000000000..99afcdea42b2a843f164962a4b29f8f63c16e0db --- /dev/null +++ b/test/examples/md/GEOMETRY @@ -0,0 +1,2 @@ + 0.740084462274 0.045946600273 0.049790097126 -0.000187193069 0.000212525459 0.000230307582 + -0.740084462274 -0.045946600273 -0.049790097126 0.000187193069 -0.000212525459 -0.000230307582 diff --git a/test/examples/md/GEOMETRY.xyz b/test/examples/md/GEOMETRY.xyz new 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70.0 +&END + +&DFT + FUNCTIONAL LDA +&END + +&ATOMS +*H_MT_LDA.psp + LMAX=S + 2 + 0.371 0.000 0.000 +-0.371 0.000 0.000 +&END + diff --git a/test/examples/md/output.out b/test/examples/md/output.out new file mode 100644 index 0000000000000000000000000000000000000000..b625a45fff05a02658c881cdd8fe97631662722b --- /dev/null +++ b/test/examples/md/output.out @@ -0,0 +1,374 @@ + cp_groups: we are using a 1 x 1 grid (groups x nprocs). + PROGRAM CPMD STARTED AT: 2016-07-25 17:12:06.301 + SETCNST| USING: CODATA 2006 UNITS + + + ****** ****** **** **** ****** + ******* ******* ********** ******* + *** ** *** ** **** ** ** *** + ** ** *** ** ** ** ** ** + ** ******* ** ** ** ** + *** ****** ** ** ** *** + ******* ** ** ** ******* + ****** ** ** ** ****** + + VERSION 4.1-rUnversioned directory + + COPYRIGHT + IBM RESEARCH DIVISION + MPI FESTKOERPERFORSCHUNG STUTTGART + + The CPMD consortium + Home Page: http://www.cpmd.org + Mailing List: cpmd-list@cpmd.org + E-mail: cpmd@cpmd.org + + + *** Jun 22 2016 -- 12:41:05 *** + + THE INPUT FILE IS: input.inp + THIS JOB RUNS ON: lenovo700 + THE CURRENT DIRECTORY IS: + /home/lauri/Dropbox/nomad-dev/nomad-lab-base/parsers/cpmd/test/unittests/cpmd_4.1/md/nve + THE TEMPORARY DIRECTORY IS: + /home/lauri/Dropbox/nomad-dev/nomad-lab-base/parsers/cpmd/test/unittests/cpmd_4.1/md/nve + THE PROCESS ID IS: 25046 + THE JOB WAS SUBMITTED BY: lauri + + + ****************************************************************************** + * INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO * + ****************************************************************************** + * isolated hydrogen molecule. * + * simple molecular dynamics deltat=4au * + ****************************************************************************** + + CAR-PARRINELLO MOLECULAR DYNAMICS + + USING SEED 123456 TO INIT. PSEUDO RANDOM NUMBER GEN. + PATH TO THE RESTART FILES: ./ + ITERATIVE ORTHOGONALIZATION + MAXIT: 30 + EPS: 1.00E-06 + MAXIMUM NUMBER OF STEPS: 50 STEPS + MAXIMUM NUMBER OF ITERATIONS FOR SC: 10000 STEPS + PRINT INTERMEDIATE RESULTS EVERY 10001 STEPS + STORE INTERMEDIATE RESULTS EVERY 10001 STEPS + STORE INTERMEDIATE RESULTS EVERY 10001 SELF-CONSISTENT STEPS + NUMBER OF DISTINCT RESTART FILES: 1 + TEMPERATURE IS CALCULATED ASSUMING EXTENDED BULK BEHAVIOR + FICTITIOUS ELECTRON MASS: 400.0000 + TIME STEP FOR ELECTRONS: 4.0000 + TIME STEP FOR IONS: 4.0000 + TRAJECTORIES ARE SAVED ON FILE + TRAJEC.xyz IS SAVED ON FILE + ELECTRON DYNAMICS: THE TEMPERATURE IS NOT CONTROLLED + ION DYNAMICS: THE TEMPERATURE IS NOT CONTROLLED + SPLINE INTERPOLATION IN G-SPACE FOR PSEUDOPOTENTIAL FUNCTIONS + NUMBER OF SPLINE POINTS: 5000 + + EXCHANGE CORRELATION FUNCTIONALS + LDA EXCHANGE: NONE + LDA XC THROUGH PADE APPROXIMATION + S.GOEDECKER, J.HUTTER, M.TETER PRB 541703 (1996) + + *** DETSP| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + + ***************************** ATOMS **************************** + NR TYPE X(BOHR) Y(BOHR) Z(BOHR) MBL + 1 H 0.701088 0.000000 0.000000 3 + 2 H -0.701088 0.000000 0.000000 3 + **************************************************************** + + NUMBER OF STATES: 1 + NUMBER OF ELECTRONS: 2.00000 + CHARGE: 0.00000 + ELECTRON TEMPERATURE(KELVIN): 0.00000 + OCCUPATION + 2.0 + + ============================================================ + | Pseudopotential Report Thu Jan 11 18:21:49 1996 | + ------------------------------------------------------------ + | Atomic Symbol : H | + | Atomic Number : 1 | + | Number of core states : 0 | + | Number of valence states : 1 | + | Exchange-Correlation Functional : | + | Slater exchange : .6667 | + | LDA correlation : Ceperley-Alder | + | Electron Configuration : N L Occupation | + | 1 S 1.0000 | + | Full Potential Total Energy -.445894 | + | Trouiller-Martins normconserving PP | + | n l rc energy | + | 1 S .5000 -.23366 | + | 2 P .5000 -.23366 | + | Number of Mesh Points : 511 | + | Pseudoatom Total Energy -.445889 | + ============================================================ + + **************************************************************** + * ATOM MASS RAGGIO NLCC PSEUDOPOTENTIAL * + * H 1.0080 1.2000 NO S LOCAL * + **************************************************************** + + + PARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARA + NCPU NGW NHG PLANES GXRAYS HXRAYS ORBITALS Z-PLANES + 0 17133 136605 90 1281 5089 1 1 + G=0 COMPONENT ON PROCESSOR : 0 + PARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARA + + *** loadpa| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + + OPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPEN + NUMBER OF CPUS PER TASK 1 + OPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPEN + + *** rggen| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + + ************************** SUPERCELL *************************** + SYMMETRY: SIMPLE CUBIC + LATTICE CONSTANT(a.u.): 15.11781 + CELL DIMENSION: 15.1178 1.0000 1.0000 0.0000 0.0000 0.0000 + VOLUME(OMEGA IN BOHR^3): 3455.14726 + LATTICE VECTOR A1(BOHR): 15.1178 0.0000 0.0000 + LATTICE VECTOR A2(BOHR): 0.0000 15.1178 0.0000 + LATTICE VECTOR A3(BOHR): 0.0000 0.0000 15.1178 + RECIP. LAT. VEC. B1(2Pi/BOHR): 0.0661 0.0000 0.0000 + RECIP. LAT. VEC. B2(2Pi/BOHR): 0.0000 0.0661 0.0000 + RECIP. LAT. VEC. B3(2Pi/BOHR): 0.0000 0.0000 0.0661 + REAL SPACE MESH: 90 90 90 + WAVEFUNCTION CUTOFF(RYDBERG): 70.00000 + DENSITY CUTOFF(RYDBERG): (DUAL= 4.00) 280.00000 + NUMBER OF PLANE WAVES FOR WAVEFUNCTION CUTOFF: 17133 + NUMBER OF PLANE WAVES FOR DENSITY CUTOFF: 136605 + **************************************************************** + + *** RINFORCE| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + *** FFTPRP| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + + GENERATE ATOMIC BASIS SET + H SLATER ORBITALS + 1S ALPHA= 1.0000 OCCUPATION= 1.00 + + + INITIALIZATION TIME: 0.48 SECONDS + + *** MDPT| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + *** PHFAC| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + NOTE: ATOMIC GUESS USING DISTRIBUTED LINALG WITH LANCZOS + *** ATOMWF| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + ATRHO| CHARGE(R-SPACE): 2.000000 (G-SPACE): 2.000000 + + **************************************************************** + * ATOMIC COORDINATES * + **************************************************************** + 1 H 0.701088 0.000000 0.000000 + 2 H -0.701088 0.000000 0.000000 + **************************************************************** + + + DEGREES OF FREEDOM FOR SYSTEM: 3 + + RVSCAL| RESCALING IONIC TEMP FROM 50.00000 TO 50.00000 + ================================================================ + == FORCES INITIALIZATION == + ================================================================ + EWALD| SUM IN REAL SPACE OVER 1* 1* 1 CELLS + + **************************************************************** + * ATOMIC COORDINATES * + **************************************************************** + 1 H 0.701088 0.000000 0.000000 + 2 H -0.701088 0.000000 0.000000 + **************************************************************** + + ================================================================ + == END OF FORCES INITIALIZATION == + ================================================================ + + TIME FOR INITIALIZATION: 1.07 SECONDS + + **************************************************************** + * ATOMIC COORDINATES * + **************************************************************** + 1 H 0.702013 0.000966 0.001047 + 2 H -0.702013 -0.000966 -0.001047 + **************************************************************** + + + TOTAL INTEGRATED ELECTRONIC DENSITY + IN G-SPACE = 2.0000000000 + IN R-SPACE = 2.0000000000 + + (K+E1+L+N+X) TOTAL ENERGY = -1.10234921 A.U. + (K) KINETIC ENERGY = 0.83136071 A.U. + (E1=A-S+R) ELECTROSTATIC ENERGY = -0.48680398 A.U. + (S) ESELF = 0.66490380 A.U. + (R) ESR = 0.17235462 A.U. + (L) LOCAL PSEUDOPOTENTIAL ENERGY = -0.86930120 A.U. + (N) N-L PSEUDOPOTENTIAL ENERGY = 0.00000000 A.U. + (X) EXCHANGE-CORRELATION ENERGY = -0.57760473 A.U. + + NFI EKINC TEMPP EKS ECLASSIC EHAM DIS TCPU + 1 0.00473 110.1 -1.10235 -1.10183 -1.09710 0.289E-05 0.25 + 2 0.01424 232.5 -1.11287 -1.11176 -1.09752 0.182E-04 0.25 + 3 0.02229 352.0 -1.12169 -1.12002 -1.09773 0.596E-04 0.25 + 4 0.02592 412.6 -1.12562 -1.12366 -1.09774 0.138E-03 0.24 + 5 0.02507 393.2 -1.12453 -1.12267 -1.09759 0.252E-03 0.23 + 6 0.02170 311.4 -1.12061 -1.11913 -1.09743 0.390E-03 0.24 + 7 0.01807 208.9 -1.11639 -1.11540 -1.09733 0.531E-03 0.23 + 8 0.01550 123.5 -1.11340 -1.11281 -1.09731 0.656E-03 0.23 + 9 0.01429 71.4 -1.11196 -1.11162 -1.09733 0.755E-03 0.24 + 10 0.01412 48.7 -1.11172 -1.11149 -1.09737 0.826E-03 0.23 + 11 0.01455 43.2 -1.11215 -1.11194 -1.09739 0.876E-03 0.23 + 12 0.01522 44.1 -1.11284 -1.11263 -1.09741 0.911E-03 0.23 + 13 0.01592 45.5 -1.11355 -1.11334 -1.09742 0.942E-03 0.23 + 14 0.01655 45.6 -1.11419 -1.11397 -1.09742 0.975E-03 0.24 + 15 0.01707 44.7 -1.11470 -1.11449 -1.09742 0.101E-02 0.23 + 16 0.01747 44.0 -1.11509 -1.11489 -1.09742 0.106E-02 0.22 + 17 0.01776 44.2 -1.11539 -1.11518 -1.09742 0.112E-02 0.24 + 18 0.01796 45.8 -1.11559 -1.11538 -1.09742 0.119E-02 0.23 + 19 0.01807 48.5 -1.11571 -1.11548 -1.09742 0.128E-02 0.23 + 20 0.01809 52.3 -1.11576 -1.11551 -1.09742 0.137E-02 0.23 + 21 0.01805 56.5 -1.11574 -1.11547 -1.09742 0.148E-02 0.23 + 22 0.01795 60.9 -1.11565 -1.11536 -1.09742 0.160E-02 0.24 + 23 0.01779 65.1 -1.11552 -1.11521 -1.09741 0.173E-02 0.23 + 24 0.01760 68.7 -1.11534 -1.11502 -1.09741 0.187E-02 0.24 + 25 0.01740 71.6 -1.11515 -1.11481 -1.09741 0.202E-02 0.24 + 26 0.01719 73.7 -1.11495 -1.11460 -1.09741 0.218E-02 0.23 + 27 0.01700 74.9 -1.11476 -1.11440 -1.09741 0.235E-02 0.23 + 28 0.01683 75.1 -1.11460 -1.11424 -1.09741 0.252E-02 0.25 + 29 0.01670 74.5 -1.11446 -1.11411 -1.09740 0.270E-02 0.24 + 30 0.01661 73.1 -1.11436 -1.11402 -1.09740 0.289E-02 0.24 + 31 0.01656 71.0 -1.11430 -1.11397 -1.09741 0.307E-02 0.23 + 32 0.01651 68.3 -1.11422 -1.11390 -1.09739 0.326E-02 0.23 + 33 0.01658 65.3 -1.11429 -1.11398 -1.09740 0.346E-02 0.23 + 34 0.01675 61.9 -1.11444 -1.11415 -1.09740 0.365E-02 0.23 + 35 0.01702 58.4 -1.11468 -1.11440 -1.09738 0.384E-02 0.23 + 36 0.01763 55.0 -1.11528 -1.11502 -1.09738 0.403E-02 0.23 + 37 0.01849 51.8 -1.11616 -1.11591 -1.09743 0.421E-02 0.23 + 38 0.01897 48.9 -1.11666 -1.11643 -1.09746 0.439E-02 0.23 + 39 0.01859 46.4 -1.11626 -1.11604 -1.09745 0.457E-02 0.22 + 40 0.01745 44.4 -1.11508 -1.11486 -1.09741 0.474E-02 0.23 + 41 0.01611 43.0 -1.11369 -1.11348 -1.09738 0.490E-02 0.23 + 42 0.01516 42.0 -1.11271 -1.11251 -1.09735 0.506E-02 0.23 + 43 0.01498 41.6 -1.11253 -1.11233 -1.09736 0.521E-02 0.23 + 44 0.01550 41.7 -1.11307 -1.11287 -1.09737 0.536E-02 0.24 + 45 0.01649 42.2 -1.11410 -1.11389 -1.09740 0.550E-02 0.24 + 46 0.01752 43.2 -1.11515 -1.11494 -1.09742 0.563E-02 0.23 + 47 0.01827 44.8 -1.11591 -1.11570 -1.09743 0.576E-02 0.29 + 48 0.01864 46.7 -1.11629 -1.11607 -1.09743 0.588E-02 0.28 + 49 0.01862 49.0 -1.11627 -1.11604 -1.09742 0.600E-02 0.24 + 50 0.01841 51.5 -1.11605 -1.11580 -1.09740 0.611E-02 0.23 + + RESTART INFORMATION WRITTEN ON FILE ./RESTART.1 + + **************************************************************** + * AVERAGED QUANTITIES * + **************************************************************** + MEAN VALUE +/- RMS DEVIATION + <x> [<x^2>-<x>^2]**(1/2) + ELECTRON KINETIC ENERGY 0.017239 0.288826E-02 + IONIC TEMPERATURE 88.6689 90.3464 + DENSITY FUNCTIONAL ENERGY -1.115075 0.322126E-02 + CLASSICAL ENERGY -1.114654 0.296260E-02 + CONSERVED ENERGY -1.097415 0.889663E-04 + NOSE ENERGY ELECTRONS 0.000000 0.00000 + NOSE ENERGY IONS 0.000000 0.00000 + CONSTRAINTS ENERGY 0.000000 0.00000 + RESTRAINTS ENERGY 0.000000 0.00000 + ION DISPLACEMENT 0.260644E-02 0.193303E-02 + CPU TIME 0.2361 + + **************************************************************** + * * + * FINAL RESULTS * + * * + **************************************************************** + + **************************************************************** + * ATOMIC COORDINATES * + **************************************************************** + 1 H 0.740084 0.045947 0.049790 + 2 H -0.740084 -0.045947 -0.049790 + **************************************************************** + + + **************************************************************** + + + ELECTRONIC GRADIENT: + MAX. COMPONENT = 1.39929E-02 NORM = 2.08955E-03 + + TOTAL INTEGRATED ELECTRONIC DENSITY + IN G-SPACE = 1.9999999999 + IN R-SPACE = 1.9999999999 + + (K+E1+L+N+X) TOTAL ENERGY = -1.11604886 A.U. + (K) KINETIC ENERGY = 1.06454894 A.U. + (E1=A-S+R) ELECTROSTATIC ENERGY = -0.50409415 A.U. + (S) ESELF = 0.66490380 A.U. + (R) ESR = 0.14497305 A.U. + (L) LOCAL PSEUDOPOTENTIAL ENERGY = -1.04064388 A.U. + (N) N-L PSEUDOPOTENTIAL ENERGY = 0.00000000 A.U. + (X) EXCHANGE-CORRELATION ENERGY = -0.63585977 A.U. + + **************************************************************** + + + + **************************************************************** + * * + * TIMING * + * * + **************************************************************** + SUBROUTINE CALLS SELF TIME TOTAL TIME + AVERAGE MAXIMUM AVERAGE MAXIMUM + cpmd 1 0.00 0.00 13.36 13.36 + mdpt 1 0.00 0.00 12.89 12.89 + mdmain 1 0.02 0.02 12.89 12.89 + forcedr 51 0.00 0.00 11.98 11.98 + forces 51 0.00 0.00 11.97 11.97 + forces_a 51 0.00 0.00 9.41 9.41 + rscpot 51 0.00 0.00 9.41 9.41 + vofrho 52 0.00 0.00 8.04 8.04 + VOFRHOB 52 0.21 0.21 5.04 5.04 + INVFFTN 157 5.02 5.02 5.02 5.02 + FWFFTN 105 3.00 3.00 3.00 3.00 + VOFRHOA 52 0.12 0.12 3.00 3.00 + vpsi 53 0.26 0.26 2.65 2.65 + xcener_new 52 0.17 0.17 2.46 2.46 + mikeu 52 2.29 2.29 2.29 2.29 + rhoofr 51 0.39 0.39 1.70 1.70 + initrun 1 0.00 0.00 0.83 0.83 + rinitwf 1 0.00 0.00 0.83 0.83 + ATOMWF 1 0.00 0.00 0.83 0.83 + potfor 51 0.49 0.49 0.49 0.49 + ATRHO 1 0.35 0.35 0.40 0.40 + ppener 52 0.29 0.29 0.29 0.29 + rinit 1 0.00 0.00 0.26 0.26 + rggen 1 0.01 0.01 0.26 0.26 + loadpa 1 0.01 0.01 0.26 0.26 + EICALC 52 0.18 0.18 0.18 0.18 + NUMPW 1 0.10 0.10 0.10 0.10 + dist_ksmat 1 0.00 0.00 0.10 0.10 + RINFORCE 1 0.00 0.00 0.10 0.10 + loadpa_b 1 0.10 0.10 0.10 0.10 + loadpa_c 1 0.10 0.10 0.10 0.10 + FORMFN 1 0.10 0.10 0.10 0.10 + loadpa_a 1 0.05 0.05 0.05 0.05 + POSUPA 50 0.01 0.01 0.03 0.03 + ovlap 152 0.01 0.01 0.02 0.02 + VELUPA 100 0.02 0.02 0.02 0.02 + PHFAC 51 0.01 0.01 0.01 0.01 + RORTOG 50 0.00 0.00 0.01 0.01 + **************************************************************** + + CPU TIME : 0 HOURS 0 MINUTES 13.36 SECONDS + ELAPSED TIME : 0 HOURS 0 MINUTES 13.37 SECONDS + *** CPMD| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + + PROGRAM CPMD ENDED AT: 2016-07-25 17:12:19.667 diff --git a/test/examples/md/run.sh b/test/examples/md/run.sh new file mode 100755 index 0000000000000000000000000000000000000000..74ce0ca5a55a21a25741d586bcf4cb42c8f14590 --- /dev/null +++ b/test/examples/md/run.sh @@ -0,0 +1,3 @@ +export CPMD_PP_LIBRARY_PATH=../../ +export OMP_NUM_THREADS=1 +cpmd41 input.inp > output.out diff --git a/test/unittests/cpmd_4.1/md/dcd/ENERGIES b/test/unittests/cpmd_4.1/md/dcd/ENERGIES new file mode 100644 index 0000000000000000000000000000000000000000..3cd94f657c6274216f449d6533ca06f6441ee5e1 --- /dev/null +++ b/test/unittests/cpmd_4.1/md/dcd/ENERGIES @@ -0,0 +1,50 @@ + 1 0.00472945 110.096 -1.1023492072 -1.1018262261 -1.0970967730 0.288545E-05 0.24 + 2 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-0.04509397524877 -0.04886613330868 0.00016538618998 -0.00021385628867 -0.00023174930644 + 50 0.74008446227396 0.04594660027294 0.04979009712617 -0.00018719306900 0.00021252545941 0.00023030758250 + 50 -0.74008446227396 -0.04594660027294 -0.04979009712617 0.00018719306900 -0.00021252545941 -0.00023030758250 diff --git a/test/unittests/cpmd_4.1/md/dcd/input.inp b/test/unittests/cpmd_4.1/md/dcd/input.inp new file mode 100755 index 0000000000000000000000000000000000000000..3b5f6e58cc8169e08d9a7dda65f223948666cc8a --- /dev/null +++ b/test/unittests/cpmd_4.1/md/dcd/input.inp @@ -0,0 +1,41 @@ +&INFO +isolated hydrogen molecule. +simple molecular dynamics deltat=4au +&END + +&CPMD + MOLECULAR DYNAMICS CP + + TRAJECTORY DCD + + TEMPERATURE + 50.0D0 + + MAXSTEP + 50 + TIMESTEP + 4.0 +&END + +&SYSTEM + SYMMETRY + 1 + ANGSTROM + CELL + 8.00 1.0 1.0 0.0 0.0 0.0 + CUTOFF + 70.0 +&END + +&DFT + FUNCTIONAL LDA +&END + +&ATOMS +*H_MT_LDA.psp + LMAX=S + 2 + 0.371 0.000 0.000 +-0.371 0.000 0.000 +&END + diff --git a/test/unittests/cpmd_4.1/md/dcd/output.out b/test/unittests/cpmd_4.1/md/dcd/output.out new file mode 100644 index 0000000000000000000000000000000000000000..b0c9787d3951165b0d4048e0c16dc0311f557c4d --- /dev/null +++ b/test/unittests/cpmd_4.1/md/dcd/output.out @@ -0,0 +1,375 @@ + cp_groups: we are using a 1 x 1 grid (groups x nprocs). + PROGRAM CPMD STARTED AT: 2016-07-26 14:19:39.304 + SETCNST| USING: CODATA 2006 UNITS + + + ****** ****** **** **** ****** + ******* ******* ********** ******* + *** ** *** ** **** ** ** *** + ** ** *** ** ** ** ** ** + ** ******* ** ** ** ** + *** ****** ** ** ** *** + ******* ** ** ** ******* + ****** ** ** ** ****** + + VERSION 4.1-rUnversioned directory + + COPYRIGHT + IBM RESEARCH DIVISION + MPI FESTKOERPERFORSCHUNG STUTTGART + + The CPMD consortium + Home Page: http://www.cpmd.org + Mailing List: cpmd-list@cpmd.org + E-mail: cpmd@cpmd.org + + + *** Jun 22 2016 -- 12:41:05 *** + + THE INPUT FILE IS: input.inp + THIS JOB RUNS ON: lenovo700 + THE CURRENT DIRECTORY IS: + /home/lauri/Dropbox/nomad-dev/nomad-lab-base/parsers/cpmd/test/unittests/cpmd_4.1/md/dcd + THE TEMPORARY DIRECTORY IS: + /home/lauri/Dropbox/nomad-dev/nomad-lab-base/parsers/cpmd/test/unittests/cpmd_4.1/md/dcd + THE PROCESS ID IS: 10925 + THE JOB WAS SUBMITTED BY: lauri + + + ****************************************************************************** + * INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO * + ****************************************************************************** + * isolated hydrogen molecule. * + * simple molecular dynamics deltat=4au * + ****************************************************************************** + + CAR-PARRINELLO MOLECULAR DYNAMICS + + USING SEED 123456 TO INIT. PSEUDO RANDOM NUMBER GEN. + PATH TO THE RESTART FILES: ./ + ITERATIVE ORTHOGONALIZATION + MAXIT: 30 + EPS: 1.00E-06 + MAXIMUM NUMBER OF STEPS: 50 STEPS + MAXIMUM NUMBER OF ITERATIONS FOR SC: 10000 STEPS + PRINT INTERMEDIATE RESULTS EVERY 10001 STEPS + STORE INTERMEDIATE RESULTS EVERY 10001 STEPS + STORE INTERMEDIATE RESULTS EVERY 10001 SELF-CONSISTENT STEPS + NUMBER OF DISTINCT RESTART FILES: 1 + TEMPERATURE IS CALCULATED ASSUMING EXTENDED BULK BEHAVIOR + FICTITIOUS ELECTRON MASS: 400.0000 + TIME STEP FOR ELECTRONS: 4.0000 + TIME STEP FOR IONS: 4.0000 + TRAJECTORIES ARE SAVED ON FILE + TRAJEC.dcd IS SAVED ON FILE + ELECTRON DYNAMICS: THE TEMPERATURE IS NOT CONTROLLED + ION DYNAMICS: THE TEMPERATURE IS NOT CONTROLLED + SPLINE INTERPOLATION IN G-SPACE FOR PSEUDOPOTENTIAL FUNCTIONS + NUMBER OF SPLINE POINTS: 5000 + + EXCHANGE CORRELATION FUNCTIONALS + LDA EXCHANGE: NONE + LDA XC THROUGH PADE APPROXIMATION + S.GOEDECKER, J.HUTTER, M.TETER PRB 541703 (1996) + + *** DETSP| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + + ***************************** ATOMS **************************** + NR TYPE X(BOHR) Y(BOHR) Z(BOHR) MBL + 1 H 0.701088 0.000000 0.000000 3 + 2 H -0.701088 0.000000 0.000000 3 + **************************************************************** + + NUMBER OF STATES: 1 + NUMBER OF ELECTRONS: 2.00000 + CHARGE: 0.00000 + ELECTRON TEMPERATURE(KELVIN): 0.00000 + OCCUPATION + 2.0 + + ============================================================ + | Pseudopotential Report Thu Jan 11 18:21:49 1996 | + ------------------------------------------------------------ + | Atomic Symbol : H | + | Atomic Number : 1 | + | Number of core states : 0 | + | Number of valence states : 1 | + | Exchange-Correlation Functional : | + | Slater exchange : .6667 | + | LDA correlation : Ceperley-Alder | + | Electron Configuration : N L Occupation | + | 1 S 1.0000 | + | Full Potential Total Energy -.445894 | + | Trouiller-Martins normconserving PP | + | n l rc energy | + | 1 S .5000 -.23366 | + | 2 P .5000 -.23366 | + | Number of Mesh Points : 511 | + | Pseudoatom Total Energy -.445889 | + ============================================================ + + **************************************************************** + * ATOM MASS RAGGIO NLCC PSEUDOPOTENTIAL * + * H 1.0080 1.2000 NO S LOCAL * + **************************************************************** + + + PARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARA + NCPU NGW NHG PLANES GXRAYS HXRAYS ORBITALS Z-PLANES + 0 17133 136605 90 1281 5089 1 1 + G=0 COMPONENT ON PROCESSOR : 0 + PARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARA + + *** loadpa| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + + OPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPEN + NUMBER OF CPUS PER TASK 1 + OPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPEN + + *** rggen| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + + ************************** SUPERCELL *************************** + SYMMETRY: SIMPLE CUBIC + LATTICE CONSTANT(a.u.): 15.11781 + CELL DIMENSION: 15.1178 1.0000 1.0000 0.0000 0.0000 0.0000 + VOLUME(OMEGA IN BOHR^3): 3455.14726 + LATTICE VECTOR A1(BOHR): 15.1178 0.0000 0.0000 + LATTICE VECTOR A2(BOHR): 0.0000 15.1178 0.0000 + LATTICE VECTOR A3(BOHR): 0.0000 0.0000 15.1178 + RECIP. LAT. VEC. B1(2Pi/BOHR): 0.0661 0.0000 0.0000 + RECIP. LAT. VEC. B2(2Pi/BOHR): 0.0000 0.0661 0.0000 + RECIP. LAT. VEC. B3(2Pi/BOHR): 0.0000 0.0000 0.0661 + REAL SPACE MESH: 90 90 90 + WAVEFUNCTION CUTOFF(RYDBERG): 70.00000 + DENSITY CUTOFF(RYDBERG): (DUAL= 4.00) 280.00000 + NUMBER OF PLANE WAVES FOR WAVEFUNCTION CUTOFF: 17133 + NUMBER OF PLANE WAVES FOR DENSITY CUTOFF: 136605 + **************************************************************** + + *** RINFORCE| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + *** FFTPRP| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + + GENERATE ATOMIC BASIS SET + H SLATER ORBITALS + 1S ALPHA= 1.0000 OCCUPATION= 1.00 + + + INITIALIZATION TIME: 0.50 SECONDS + + *** MDPT| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + *** PHFAC| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + NOTE: ATOMIC GUESS USING DISTRIBUTED LINALG WITH LANCZOS + *** ATOMWF| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + ATRHO| CHARGE(R-SPACE): 2.000000 (G-SPACE): 2.000000 + + **************************************************************** + * ATOMIC COORDINATES * + **************************************************************** + 1 H 0.701088 0.000000 0.000000 + 2 H -0.701088 0.000000 0.000000 + **************************************************************** + + + DEGREES OF FREEDOM FOR SYSTEM: 3 + + RVSCAL| RESCALING IONIC TEMP FROM 50.00000 TO 50.00000 + ================================================================ + == FORCES INITIALIZATION == + ================================================================ + EWALD| SUM IN REAL SPACE OVER 1* 1* 1 CELLS + + **************************************************************** + * ATOMIC COORDINATES * + **************************************************************** + 1 H 0.701088 0.000000 0.000000 + 2 H -0.701088 0.000000 0.000000 + **************************************************************** + + ================================================================ + == END OF FORCES INITIALIZATION == + ================================================================ + + TIME FOR INITIALIZATION: 1.06 SECONDS + + **************************************************************** + * ATOMIC COORDINATES * + **************************************************************** + 1 H 0.702013 0.000966 0.001047 + 2 H -0.702013 -0.000966 -0.001047 + **************************************************************** + + + TOTAL INTEGRATED ELECTRONIC DENSITY + IN G-SPACE = 2.0000000000 + IN R-SPACE = 2.0000000000 + + (K+E1+L+N+X) TOTAL ENERGY = -1.10234921 A.U. + (K) KINETIC ENERGY = 0.83136071 A.U. + (E1=A-S+R) ELECTROSTATIC ENERGY = -0.48680398 A.U. + (S) ESELF = 0.66490380 A.U. + (R) ESR = 0.17235462 A.U. + (L) LOCAL PSEUDOPOTENTIAL ENERGY = -0.86930120 A.U. + (N) N-L PSEUDOPOTENTIAL ENERGY = 0.00000000 A.U. + (X) EXCHANGE-CORRELATION ENERGY = -0.57760473 A.U. + + NFI EKINC TEMPP EKS ECLASSIC EHAM DIS TCPU + 1 0.00473 110.1 -1.10235 -1.10183 -1.09710 0.289E-05 0.24 + FILE TRAJEC.dcd EXISTS, NEW DATA WILL BE APPENDED + 2 0.01424 232.5 -1.11287 -1.11176 -1.09752 0.182E-04 0.25 + 3 0.02229 352.0 -1.12169 -1.12002 -1.09773 0.596E-04 0.23 + 4 0.02592 412.6 -1.12562 -1.12366 -1.09774 0.138E-03 0.24 + 5 0.02507 393.2 -1.12453 -1.12267 -1.09759 0.252E-03 0.23 + 6 0.02170 311.4 -1.12061 -1.11913 -1.09743 0.390E-03 0.23 + 7 0.01807 208.9 -1.11639 -1.11540 -1.09733 0.531E-03 0.24 + 8 0.01550 123.5 -1.11340 -1.11281 -1.09731 0.656E-03 0.23 + 9 0.01429 71.4 -1.11196 -1.11162 -1.09733 0.755E-03 0.23 + 10 0.01412 48.7 -1.11172 -1.11149 -1.09737 0.826E-03 0.23 + 11 0.01455 43.2 -1.11215 -1.11194 -1.09739 0.876E-03 0.23 + 12 0.01522 44.1 -1.11284 -1.11263 -1.09741 0.911E-03 0.23 + 13 0.01592 45.5 -1.11355 -1.11334 -1.09742 0.942E-03 0.23 + 14 0.01655 45.6 -1.11419 -1.11397 -1.09742 0.975E-03 0.22 + 15 0.01707 44.7 -1.11470 -1.11449 -1.09742 0.101E-02 0.24 + 16 0.01747 44.0 -1.11509 -1.11489 -1.09742 0.106E-02 0.22 + 17 0.01776 44.2 -1.11539 -1.11518 -1.09742 0.112E-02 0.23 + 18 0.01796 45.8 -1.11559 -1.11538 -1.09742 0.119E-02 0.23 + 19 0.01807 48.5 -1.11571 -1.11548 -1.09742 0.128E-02 0.22 + 20 0.01809 52.3 -1.11576 -1.11551 -1.09742 0.137E-02 0.23 + 21 0.01805 56.5 -1.11574 -1.11547 -1.09742 0.148E-02 0.23 + 22 0.01795 60.9 -1.11565 -1.11536 -1.09742 0.160E-02 0.23 + 23 0.01779 65.1 -1.11552 -1.11521 -1.09741 0.173E-02 0.23 + 24 0.01760 68.7 -1.11534 -1.11502 -1.09741 0.187E-02 0.23 + 25 0.01740 71.6 -1.11515 -1.11481 -1.09741 0.202E-02 0.23 + 26 0.01719 73.7 -1.11495 -1.11460 -1.09741 0.218E-02 0.24 + 27 0.01700 74.9 -1.11476 -1.11440 -1.09741 0.235E-02 0.23 + 28 0.01683 75.1 -1.11460 -1.11424 -1.09741 0.252E-02 0.23 + 29 0.01670 74.5 -1.11446 -1.11411 -1.09740 0.270E-02 0.23 + 30 0.01661 73.1 -1.11436 -1.11402 -1.09740 0.289E-02 0.23 + 31 0.01656 71.0 -1.11430 -1.11397 -1.09741 0.307E-02 0.23 + 32 0.01651 68.3 -1.11422 -1.11390 -1.09739 0.326E-02 0.23 + 33 0.01658 65.3 -1.11429 -1.11398 -1.09740 0.346E-02 0.23 + 34 0.01675 61.9 -1.11444 -1.11415 -1.09740 0.365E-02 0.23 + 35 0.01702 58.4 -1.11468 -1.11440 -1.09738 0.384E-02 0.23 + 36 0.01763 55.0 -1.11528 -1.11502 -1.09738 0.403E-02 0.23 + 37 0.01849 51.8 -1.11616 -1.11591 -1.09743 0.421E-02 0.23 + 38 0.01897 48.9 -1.11666 -1.11643 -1.09746 0.439E-02 0.23 + 39 0.01859 46.4 -1.11626 -1.11604 -1.09745 0.457E-02 0.23 + 40 0.01745 44.4 -1.11508 -1.11486 -1.09741 0.474E-02 0.22 + 41 0.01611 43.0 -1.11369 -1.11348 -1.09738 0.490E-02 0.23 + 42 0.01516 42.0 -1.11271 -1.11251 -1.09735 0.506E-02 0.23 + 43 0.01498 41.6 -1.11253 -1.11233 -1.09736 0.521E-02 0.22 + 44 0.01550 41.7 -1.11307 -1.11287 -1.09737 0.536E-02 0.23 + 45 0.01649 42.2 -1.11410 -1.11389 -1.09740 0.550E-02 0.22 + 46 0.01752 43.2 -1.11515 -1.11494 -1.09742 0.563E-02 0.23 + 47 0.01827 44.8 -1.11591 -1.11570 -1.09743 0.576E-02 0.22 + 48 0.01864 46.7 -1.11629 -1.11607 -1.09743 0.588E-02 0.23 + 49 0.01862 49.0 -1.11627 -1.11604 -1.09742 0.600E-02 0.22 + 50 0.01841 51.5 -1.11605 -1.11580 -1.09740 0.611E-02 0.22 + + RESTART INFORMATION WRITTEN ON FILE ./RESTART.1 + + **************************************************************** + * AVERAGED QUANTITIES * + **************************************************************** + MEAN VALUE +/- RMS DEVIATION + <x> [<x^2>-<x>^2]**(1/2) + ELECTRON KINETIC ENERGY 0.017239 0.288826E-02 + IONIC TEMPERATURE 88.6689 90.3464 + DENSITY FUNCTIONAL ENERGY -1.115075 0.322126E-02 + CLASSICAL ENERGY -1.114654 0.296260E-02 + CONSERVED ENERGY -1.097415 0.889663E-04 + NOSE ENERGY ELECTRONS 0.000000 0.00000 + NOSE ENERGY IONS 0.000000 0.00000 + CONSTRAINTS ENERGY 0.000000 0.00000 + RESTRAINTS ENERGY 0.000000 0.00000 + ION DISPLACEMENT 0.260644E-02 0.193303E-02 + CPU TIME 0.2288 + + **************************************************************** + * * + * FINAL RESULTS * + * * + **************************************************************** + + **************************************************************** + * ATOMIC COORDINATES * + **************************************************************** + 1 H 0.740084 0.045947 0.049790 + 2 H -0.740084 -0.045947 -0.049790 + **************************************************************** + + + **************************************************************** + + + ELECTRONIC GRADIENT: + MAX. COMPONENT = 1.39929E-02 NORM = 2.08955E-03 + + TOTAL INTEGRATED ELECTRONIC DENSITY + IN G-SPACE = 1.9999999999 + IN R-SPACE = 1.9999999999 + + (K+E1+L+N+X) TOTAL ENERGY = -1.11604886 A.U. + (K) KINETIC ENERGY = 1.06454894 A.U. + (E1=A-S+R) ELECTROSTATIC ENERGY = -0.50409415 A.U. + (S) ESELF = 0.66490380 A.U. + (R) ESR = 0.14497305 A.U. + (L) LOCAL PSEUDOPOTENTIAL ENERGY = -1.04064388 A.U. + (N) N-L PSEUDOPOTENTIAL ENERGY = 0.00000000 A.U. + (X) EXCHANGE-CORRELATION ENERGY = -0.63585977 A.U. + + **************************************************************** + + + + **************************************************************** + * * + * TIMING * + * * + **************************************************************** + SUBROUTINE CALLS SELF TIME TOTAL TIME + AVERAGE MAXIMUM AVERAGE MAXIMUM + cpmd 1 0.01 0.01 13.00 13.00 + mdpt 1 0.00 0.00 12.51 12.51 + mdmain 1 0.02 0.02 12.51 12.51 + forcedr 51 0.00 0.00 11.60 11.60 + forces 51 0.01 0.01 11.60 11.60 + forces_a 51 0.00 0.00 9.10 9.10 + rscpot 51 0.00 0.00 9.10 9.10 + vofrho 52 0.00 0.00 7.79 7.79 + VOFRHOB 52 0.19 0.19 4.89 4.89 + INVFFTN 157 4.84 4.84 4.84 4.84 + FWFFTN 105 2.93 2.93 2.93 2.93 + VOFRHOA 52 0.12 0.12 2.90 2.90 + vpsi 53 0.26 0.26 2.59 2.59 + xcener_new 52 0.18 0.18 2.41 2.41 + mikeu 52 2.24 2.24 2.24 2.24 + rhoofr 51 0.37 0.37 1.62 1.62 + initrun 1 0.00 0.00 0.82 0.82 + rinitwf 1 0.00 0.00 0.81 0.81 + ATOMWF 1 0.00 0.00 0.81 0.81 + potfor 51 0.46 0.46 0.46 0.46 + ATRHO 1 0.36 0.36 0.40 0.40 + ppener 52 0.28 0.28 0.28 0.28 + rinit 1 0.00 0.00 0.26 0.26 + rggen 1 0.01 0.01 0.26 0.26 + loadpa 1 0.01 0.01 0.25 0.25 + EICALC 52 0.18 0.18 0.18 0.18 + NUMPW 1 0.12 0.12 0.12 0.12 + RINFORCE 1 0.00 0.00 0.10 0.10 + loadpa_b 1 0.10 0.10 0.10 0.10 + dist_ksmat 1 0.00 0.00 0.10 0.10 + FORMFN 1 0.10 0.10 0.10 0.10 + loadpa_c 1 0.09 0.09 0.09 0.09 + loadpa_a 1 0.04 0.04 0.04 0.04 + POSUPA 50 0.01 0.01 0.03 0.03 + ovlap 152 0.01 0.01 0.02 0.02 + ROTATE 152 0.01 0.01 0.01 0.01 + ovlap_grps_a 152 0.01 0.01 0.01 0.01 + PHFAC 51 0.01 0.01 0.01 0.01 + **************************************************************** + + CPU TIME : 0 HOURS 0 MINUTES 12.98 SECONDS + ELAPSED TIME : 0 HOURS 0 MINUTES 13.00 SECONDS + *** CPMD| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + + PROGRAM CPMD ENDED AT: 2016-07-26 14:19:52.304 diff --git a/test/unittests/cpmd_4.1/md/dcd/run.sh b/test/unittests/cpmd_4.1/md/dcd/run.sh new file mode 100755 index 0000000000000000000000000000000000000000..74ce0ca5a55a21a25741d586bcf4cb42c8f14590 --- /dev/null +++ b/test/unittests/cpmd_4.1/md/dcd/run.sh @@ -0,0 +1,3 @@ +export CPMD_PP_LIBRARY_PATH=../../ +export OMP_NUM_THREADS=1 +cpmd41 input.inp > output.out diff --git a/test/unittests/cpmd_4.1/md/forces/ENERGIES b/test/unittests/cpmd_4.1/md/forces/ENERGIES new file mode 100644 index 0000000000000000000000000000000000000000..ca09719898e9b6af84d59683ab5558f8438638f3 --- /dev/null +++ b/test/unittests/cpmd_4.1/md/forces/ENERGIES @@ -0,0 +1,50 @@ + 1 0.00472945 110.096 -1.1023492072 -1.1018262261 -1.0970967730 0.288545E-05 0.25 + 2 0.01424065 232.496 -1.1128688938 -1.1117644858 -1.0975238350 0.182162E-04 0.24 + 3 0.02228702 351.956 -1.1216882365 -1.1200163669 -1.0977293448 0.596327E-04 0.23 + 4 0.02592222 412.578 -1.1256188624 -1.1236590243 -1.0977368045 0.137607E-03 0.23 + 5 0.02507375 393.180 -1.1245335482 -1.1226658551 -1.0975921059 0.251896E-03 0.27 + 6 0.02170348 311.439 -1.1206087528 -1.1191293469 -1.0974258636 0.389716E-03 0.26 + 7 0.01806912 208.928 -1.1163887071 -1.1153962539 -1.0973271357 0.530786E-03 0.23 + 8 0.01550309 123.508 -1.1133979574 -1.1128112667 -1.0973081718 0.656212E-03 0.23 + 9 0.01428927 71.351 -1.1119610076 -1.1116220739 -1.0973328023 0.755177E-03 0.23 + 10 0.01412005 48.653 -1.1117171754 -1.1114860650 -1.0973660187 0.826435E-03 0.23 + 11 0.01454963 43.205 -1.1121477411 -1.1119425095 -1.0973928823 0.875667E-03 0.22 + 12 0.01522198 44.147 -1.1128400647 -1.1126303571 -1.0974083755 0.911456E-03 0.23 + 13 0.01592316 45.526 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-0.00018719306900 0.00021252545941 0.00023030758250 + 50 -0.74008446227396 -0.04594660027294 -0.04979009712617 0.00018719306900 -0.00021252545941 -0.00023030758250 diff --git a/test/unittests/cpmd_4.1/md/forces/input.inp b/test/unittests/cpmd_4.1/md/forces/input.inp new file mode 100755 index 0000000000000000000000000000000000000000..ed8782c3ade62b6b03780bfe63a7ee9690c40563 --- /dev/null +++ b/test/unittests/cpmd_4.1/md/forces/input.inp @@ -0,0 +1,41 @@ +&INFO +isolated hydrogen molecule. +simple molecular dynamics deltat=4au +&END + +&CPMD + MOLECULAR DYNAMICS CP + + TRAJECTORY XYZ FORCES + + TEMPERATURE + 50.0D0 + + MAXSTEP + 50 + TIMESTEP + 4.0 +&END + +&SYSTEM + SYMMETRY + 1 + ANGSTROM + CELL + 8.00 1.0 1.0 0.0 0.0 0.0 + CUTOFF + 70.0 +&END + +&DFT + FUNCTIONAL LDA +&END + +&ATOMS +*H_MT_LDA.psp + LMAX=S + 2 + 0.371 0.000 0.000 +-0.371 0.000 0.000 +&END + diff --git a/test/unittests/cpmd_4.1/md/forces/output.out b/test/unittests/cpmd_4.1/md/forces/output.out new file mode 100644 index 0000000000000000000000000000000000000000..e1d43a7f863436a4425ef15318b7bb95658b9e75 --- /dev/null +++ b/test/unittests/cpmd_4.1/md/forces/output.out @@ -0,0 +1,376 @@ + cp_groups: we are using a 1 x 1 grid (groups x nprocs). + PROGRAM CPMD STARTED AT: 2016-07-26 14:24:59.995 + SETCNST| USING: CODATA 2006 UNITS + + + ****** ****** **** **** ****** + ******* ******* ********** ******* + *** ** *** ** **** ** ** *** + ** ** *** ** ** ** ** ** + ** ******* ** ** ** ** + *** ****** ** ** ** *** + ******* ** ** ** ******* + ****** ** ** ** ****** + + VERSION 4.1-rUnversioned directory + + COPYRIGHT + IBM RESEARCH DIVISION + MPI FESTKOERPERFORSCHUNG STUTTGART + + The CPMD consortium + Home Page: http://www.cpmd.org + Mailing List: cpmd-list@cpmd.org + E-mail: cpmd@cpmd.org + + + *** Jun 22 2016 -- 12:41:05 *** + + THE INPUT FILE IS: input.inp + THIS JOB RUNS ON: lenovo700 + THE CURRENT DIRECTORY IS: + /home/lauri/Dropbox/nomad-dev/nomad-lab-base/parsers/cpmd/test/unittests/cpmd_4.1/md/forces + THE TEMPORARY DIRECTORY IS: + /home/lauri/Dropbox/nomad-dev/nomad-lab-base/parsers/cpmd/test/unittests/cpmd_4.1/md/forces + THE PROCESS ID IS: 11742 + THE JOB WAS SUBMITTED BY: lauri + + + ****************************************************************************** + * INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO * + ****************************************************************************** + * isolated hydrogen molecule. * + * simple molecular dynamics deltat=4au * + ****************************************************************************** + + CAR-PARRINELLO MOLECULAR DYNAMICS + + USING SEED 123456 TO INIT. PSEUDO RANDOM NUMBER GEN. + PATH TO THE RESTART FILES: ./ + ITERATIVE ORTHOGONALIZATION + MAXIT: 30 + EPS: 1.00E-06 + MAXIMUM NUMBER OF STEPS: 50 STEPS + MAXIMUM NUMBER OF ITERATIONS FOR SC: 10000 STEPS + PRINT INTERMEDIATE RESULTS EVERY 10001 STEPS + STORE INTERMEDIATE RESULTS EVERY 10001 STEPS + STORE INTERMEDIATE RESULTS EVERY 10001 SELF-CONSISTENT STEPS + NUMBER OF DISTINCT RESTART FILES: 1 + TEMPERATURE IS CALCULATED ASSUMING EXTENDED BULK BEHAVIOR + FICTITIOUS ELECTRON MASS: 400.0000 + TIME STEP FOR ELECTRONS: 4.0000 + TIME STEP FOR IONS: 4.0000 + TRAJECTORIES ARE SAVED ON FILE + TRAJEC.xyz IS SAVED ON FILE + ELECTRON DYNAMICS: THE TEMPERATURE IS NOT CONTROLLED + ION DYNAMICS: THE TEMPERATURE IS NOT CONTROLLED + SPLINE INTERPOLATION IN G-SPACE FOR PSEUDOPOTENTIAL FUNCTIONS + NUMBER OF SPLINE POINTS: 5000 + + EXCHANGE CORRELATION FUNCTIONALS + LDA EXCHANGE: NONE + LDA XC THROUGH PADE APPROXIMATION + S.GOEDECKER, J.HUTTER, M.TETER PRB 541703 (1996) + + *** DETSP| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + + ***************************** ATOMS **************************** + NR TYPE X(BOHR) Y(BOHR) Z(BOHR) MBL + 1 H 0.701088 0.000000 0.000000 3 + 2 H -0.701088 0.000000 0.000000 3 + **************************************************************** + + NUMBER OF STATES: 1 + NUMBER OF ELECTRONS: 2.00000 + CHARGE: 0.00000 + ELECTRON TEMPERATURE(KELVIN): 0.00000 + OCCUPATION + 2.0 + + ============================================================ + | Pseudopotential Report Thu Jan 11 18:21:49 1996 | + ------------------------------------------------------------ + | Atomic Symbol : H | + | Atomic Number : 1 | + | Number of core states : 0 | + | Number of valence states : 1 | + | Exchange-Correlation Functional : | + | Slater exchange : .6667 | + | LDA correlation : Ceperley-Alder | + | Electron Configuration : N L Occupation | + | 1 S 1.0000 | + | Full Potential Total Energy -.445894 | + | Trouiller-Martins normconserving PP | + | n l rc energy | + | 1 S .5000 -.23366 | + | 2 P .5000 -.23366 | + | Number of Mesh Points : 511 | + | Pseudoatom Total Energy -.445889 | + ============================================================ + + **************************************************************** + * ATOM MASS RAGGIO NLCC PSEUDOPOTENTIAL * + * H 1.0080 1.2000 NO S LOCAL * + **************************************************************** + + + PARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARA + NCPU NGW NHG PLANES GXRAYS HXRAYS ORBITALS Z-PLANES + 0 17133 136605 90 1281 5089 1 1 + G=0 COMPONENT ON PROCESSOR : 0 + PARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARA + + *** loadpa| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + + OPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPEN + NUMBER OF CPUS PER TASK 1 + OPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPEN + + *** rggen| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + + ************************** SUPERCELL *************************** + SYMMETRY: SIMPLE CUBIC + LATTICE CONSTANT(a.u.): 15.11781 + CELL DIMENSION: 15.1178 1.0000 1.0000 0.0000 0.0000 0.0000 + VOLUME(OMEGA IN BOHR^3): 3455.14726 + LATTICE VECTOR A1(BOHR): 15.1178 0.0000 0.0000 + LATTICE VECTOR A2(BOHR): 0.0000 15.1178 0.0000 + LATTICE VECTOR A3(BOHR): 0.0000 0.0000 15.1178 + RECIP. LAT. VEC. B1(2Pi/BOHR): 0.0661 0.0000 0.0000 + RECIP. LAT. VEC. B2(2Pi/BOHR): 0.0000 0.0661 0.0000 + RECIP. LAT. VEC. B3(2Pi/BOHR): 0.0000 0.0000 0.0661 + REAL SPACE MESH: 90 90 90 + WAVEFUNCTION CUTOFF(RYDBERG): 70.00000 + DENSITY CUTOFF(RYDBERG): (DUAL= 4.00) 280.00000 + NUMBER OF PLANE WAVES FOR WAVEFUNCTION CUTOFF: 17133 + NUMBER OF PLANE WAVES FOR DENSITY CUTOFF: 136605 + **************************************************************** + + *** RINFORCE| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + *** FFTPRP| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + + GENERATE ATOMIC BASIS SET + H SLATER ORBITALS + 1S ALPHA= 1.0000 OCCUPATION= 1.00 + + + INITIALIZATION TIME: 0.58 SECONDS + + *** MDPT| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + *** PHFAC| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + NOTE: ATOMIC GUESS USING DISTRIBUTED LINALG WITH LANCZOS + *** ATOMWF| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + ATRHO| CHARGE(R-SPACE): 2.000000 (G-SPACE): 2.000000 + + **************************************************************** + * ATOMIC COORDINATES * + **************************************************************** + 1 H 0.701088 0.000000 0.000000 + 2 H -0.701088 0.000000 0.000000 + **************************************************************** + + + DEGREES OF FREEDOM FOR SYSTEM: 3 + + RVSCAL| RESCALING IONIC TEMP FROM 50.00000 TO 50.00000 + ================================================================ + == FORCES INITIALIZATION == + ================================================================ + EWALD| SUM IN REAL SPACE OVER 1* 1* 1 CELLS + + **************************************************************** + * ATOMIC COORDINATES * + **************************************************************** + 1 H 0.701088 0.000000 0.000000 + 2 H -0.701088 0.000000 0.000000 + **************************************************************** + + ================================================================ + == END OF FORCES INITIALIZATION == + ================================================================ + + TIME FOR INITIALIZATION: 1.17 SECONDS + + **************************************************************** + * ATOMIC COORDINATES * + **************************************************************** + 1 H 0.702013 0.000966 0.001047 + 2 H -0.702013 -0.000966 -0.001047 + **************************************************************** + + + TOTAL INTEGRATED ELECTRONIC DENSITY + IN G-SPACE = 2.0000000000 + IN R-SPACE = 2.0000000000 + + (K+E1+L+N+X) TOTAL ENERGY = -1.10234921 A.U. + (K) KINETIC ENERGY = 0.83136071 A.U. + (E1=A-S+R) ELECTROSTATIC ENERGY = -0.48680398 A.U. + (S) ESELF = 0.66490380 A.U. + (R) ESR = 0.17235462 A.U. + (L) LOCAL PSEUDOPOTENTIAL ENERGY = -0.86930120 A.U. + (N) N-L PSEUDOPOTENTIAL ENERGY = 0.00000000 A.U. + (X) EXCHANGE-CORRELATION ENERGY = -0.57760473 A.U. + + NFI EKINC TEMPP EKS ECLASSIC EHAM DIS TCPU + 1 0.00473 110.1 -1.10235 -1.10183 -1.09710 0.289E-05 0.25 + 2 0.01424 232.5 -1.11287 -1.11176 -1.09752 0.182E-04 0.24 + 3 0.02229 352.0 -1.12169 -1.12002 -1.09773 0.596E-04 0.23 + 4 0.02592 412.6 -1.12562 -1.12366 -1.09774 0.138E-03 0.23 + 5 0.02507 393.2 -1.12453 -1.12267 -1.09759 0.252E-03 0.27 + 6 0.02170 311.4 -1.12061 -1.11913 -1.09743 0.390E-03 0.26 + 7 0.01807 208.9 -1.11639 -1.11540 -1.09733 0.531E-03 0.23 + 8 0.01550 123.5 -1.11340 -1.11281 -1.09731 0.656E-03 0.23 + 9 0.01429 71.4 -1.11196 -1.11162 -1.09733 0.755E-03 0.23 + 10 0.01412 48.7 -1.11172 -1.11149 -1.09737 0.826E-03 0.23 + 11 0.01455 43.2 -1.11215 -1.11194 -1.09739 0.876E-03 0.22 + 12 0.01522 44.1 -1.11284 -1.11263 -1.09741 0.911E-03 0.23 + 13 0.01592 45.5 -1.11355 -1.11334 -1.09742 0.942E-03 0.23 + 14 0.01655 45.6 -1.11419 -1.11397 -1.09742 0.975E-03 0.24 + 15 0.01707 44.7 -1.11470 -1.11449 -1.09742 0.101E-02 0.23 + 16 0.01747 44.0 -1.11509 -1.11489 -1.09742 0.106E-02 0.26 + 17 0.01776 44.2 -1.11539 -1.11518 -1.09742 0.112E-02 0.32 + 18 0.01796 45.8 -1.11559 -1.11538 -1.09742 0.119E-02 0.34 + 19 0.01807 48.5 -1.11571 -1.11548 -1.09742 0.128E-02 0.31 + 20 0.01809 52.3 -1.11576 -1.11551 -1.09742 0.137E-02 0.25 + 21 0.01805 56.5 -1.11574 -1.11547 -1.09742 0.148E-02 0.23 + 22 0.01795 60.9 -1.11565 -1.11536 -1.09742 0.160E-02 0.24 + 23 0.01779 65.1 -1.11552 -1.11521 -1.09741 0.173E-02 0.24 + 24 0.01760 68.7 -1.11534 -1.11502 -1.09741 0.187E-02 0.31 + 25 0.01740 71.6 -1.11515 -1.11481 -1.09741 0.202E-02 0.31 + 26 0.01719 73.7 -1.11495 -1.11460 -1.09741 0.218E-02 0.31 + 27 0.01700 74.9 -1.11476 -1.11440 -1.09741 0.235E-02 0.30 + 28 0.01683 75.1 -1.11460 -1.11424 -1.09741 0.252E-02 0.26 + 29 0.01670 74.5 -1.11446 -1.11411 -1.09740 0.270E-02 0.24 + 30 0.01661 73.1 -1.11436 -1.11402 -1.09740 0.289E-02 0.24 + 31 0.01656 71.0 -1.11430 -1.11397 -1.09741 0.307E-02 0.24 + 32 0.01651 68.3 -1.11422 -1.11390 -1.09739 0.326E-02 0.26 + 33 0.01658 65.3 -1.11429 -1.11398 -1.09740 0.346E-02 0.25 + 34 0.01675 61.9 -1.11444 -1.11415 -1.09740 0.365E-02 0.25 + 35 0.01702 58.4 -1.11468 -1.11440 -1.09738 0.384E-02 0.25 + 36 0.01763 55.0 -1.11528 -1.11502 -1.09738 0.403E-02 0.24 + 37 0.01849 51.8 -1.11616 -1.11591 -1.09743 0.421E-02 0.24 + 38 0.01897 48.9 -1.11666 -1.11643 -1.09746 0.439E-02 0.23 + 39 0.01859 46.4 -1.11626 -1.11604 -1.09745 0.457E-02 0.24 + 40 0.01745 44.4 -1.11508 -1.11486 -1.09741 0.474E-02 0.23 + 41 0.01611 43.0 -1.11369 -1.11348 -1.09738 0.490E-02 0.24 + 42 0.01516 42.0 -1.11271 -1.11251 -1.09735 0.506E-02 0.24 + 43 0.01498 41.6 -1.11253 -1.11233 -1.09736 0.521E-02 0.24 + 44 0.01550 41.7 -1.11307 -1.11287 -1.09737 0.536E-02 0.24 + 45 0.01649 42.2 -1.11410 -1.11389 -1.09740 0.550E-02 0.24 + 46 0.01752 43.2 -1.11515 -1.11494 -1.09742 0.563E-02 0.24 + 47 0.01827 44.8 -1.11591 -1.11570 -1.09743 0.576E-02 0.23 + 48 0.01864 46.7 -1.11629 -1.11607 -1.09743 0.588E-02 0.24 + 49 0.01862 49.0 -1.11627 -1.11604 -1.09742 0.600E-02 0.24 + 50 0.01841 51.5 -1.11605 -1.11580 -1.09740 0.611E-02 0.23 + + RESTART INFORMATION WRITTEN ON FILE ./RESTART.1 + + **************************************************************** + * AVERAGED QUANTITIES * + **************************************************************** + MEAN VALUE +/- RMS DEVIATION + <x> [<x^2>-<x>^2]**(1/2) + ELECTRON KINETIC ENERGY 0.017239 0.288826E-02 + IONIC TEMPERATURE 88.6689 90.3464 + DENSITY FUNCTIONAL ENERGY -1.115075 0.322126E-02 + CLASSICAL ENERGY -1.114654 0.296260E-02 + CONSERVED ENERGY -1.097415 0.889663E-04 + NOSE ENERGY ELECTRONS 0.000000 0.00000 + NOSE ENERGY IONS 0.000000 0.00000 + CONSTRAINTS ENERGY 0.000000 0.00000 + RESTRAINTS ENERGY 0.000000 0.00000 + ION DISPLACEMENT 0.260644E-02 0.193303E-02 + CPU TIME 0.2502 + + **************************************************************** + * * + * FINAL RESULTS * + * * + **************************************************************** + + **************************************************************** + * ATOMIC COORDINATES * + **************************************************************** + 1 H 0.740084 0.045947 0.049790 + 2 H -0.740084 -0.045947 -0.049790 + **************************************************************** + + + **************************************************************** + + + ELECTRONIC GRADIENT: + MAX. COMPONENT = 1.39929E-02 NORM = 2.08955E-03 + + TOTAL INTEGRATED ELECTRONIC DENSITY + IN G-SPACE = 1.9999999999 + IN R-SPACE = 1.9999999999 + + (K+E1+L+N+X) TOTAL ENERGY = -1.11604886 A.U. + (K) KINETIC ENERGY = 1.06454894 A.U. + (E1=A-S+R) ELECTROSTATIC ENERGY = -0.50409415 A.U. + (S) ESELF = 0.66490380 A.U. + (R) ESR = 0.14497305 A.U. + (L) LOCAL PSEUDOPOTENTIAL ENERGY = -1.04064388 A.U. + (N) N-L PSEUDOPOTENTIAL ENERGY = 0.00000000 A.U. + (X) EXCHANGE-CORRELATION ENERGY = -0.63585977 A.U. + + **************************************************************** + + + + **************************************************************** + * * + * TIMING * + * * + **************************************************************** + SUBROUTINE CALLS SELF TIME TOTAL TIME + AVERAGE MAXIMUM AVERAGE MAXIMUM + cpmd 1 0.01 0.01 14.26 14.26 + mdpt 1 0.00 0.00 13.68 13.68 + mdmain 1 0.02 0.02 13.68 13.68 + forcedr 51 0.00 0.00 12.69 12.69 + forces 51 0.00 0.00 12.69 12.69 + forces_a 51 0.00 0.00 9.87 9.87 + rscpot 51 0.00 0.00 9.87 9.87 + vofrho 52 0.00 0.00 8.39 8.39 + INVFFTN 157 5.29 5.29 5.29 5.29 + VOFRHOB 52 0.22 0.22 5.22 5.22 + FWFFTN 105 3.21 3.21 3.21 3.21 + VOFRHOA 52 0.13 0.13 3.17 3.17 + vpsi 53 0.29 0.29 2.90 2.90 + xcener_new 52 0.19 0.19 2.58 2.58 + mikeu 52 2.38 2.38 2.38 2.38 + rhoofr 51 0.40 0.40 1.80 1.80 + initrun 1 0.00 0.00 0.91 0.91 + rinitwf 1 0.00 0.00 0.91 0.91 + ATOMWF 1 0.00 0.00 0.91 0.91 + potfor 51 0.51 0.51 0.51 0.51 + ATRHO 1 0.44 0.44 0.49 0.49 + ppener 52 0.31 0.31 0.31 0.31 + rinit 1 0.00 0.00 0.30 0.30 + rggen 1 0.01 0.01 0.30 0.30 + loadpa 1 0.02 0.02 0.30 0.30 + EICALC 52 0.20 0.20 0.20 0.20 + NUMPW 1 0.13 0.13 0.13 0.13 + RINFORCE 1 0.00 0.00 0.12 0.12 + loadpa_b 1 0.12 0.12 0.12 0.12 + FORMFN 1 0.11 0.11 0.11 0.11 + loadpa_c 1 0.11 0.11 0.11 0.11 + dist_ksmat 1 0.00 0.00 0.10 0.10 + loadpa_a 1 0.05 0.05 0.05 0.05 + POSUPA 50 0.01 0.01 0.03 0.03 + ovlap 152 0.01 0.01 0.03 0.03 + RORTOG 50 0.00 0.00 0.02 0.02 + ovlap_grps_a 152 0.02 0.02 0.02 0.02 + ROTATE 152 0.02 0.02 0.02 0.02 + PHFAC 51 0.01 0.01 0.01 0.01 + forces_b 51 0.01 0.01 0.01 0.01 + **************************************************************** + + CPU TIME : 0 HOURS 0 MINUTES 14.26 SECONDS + ELAPSED TIME : 0 HOURS 0 MINUTES 14.26 SECONDS + *** CPMD| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + + PROGRAM CPMD ENDED AT: 2016-07-26 14:25:14.254 diff --git a/test/unittests/cpmd_4.1/md/forces/run.sh b/test/unittests/cpmd_4.1/md/forces/run.sh new file mode 100755 index 0000000000000000000000000000000000000000..74ce0ca5a55a21a25741d586bcf4cb42c8f14590 --- /dev/null +++ b/test/unittests/cpmd_4.1/md/forces/run.sh @@ -0,0 +1,3 @@ +export CPMD_PP_LIBRARY_PATH=../../ +export OMP_NUM_THREADS=1 +cpmd41 input.inp > output.out diff --git a/test/unittests/cpmd_4.1/md/ntraj/ENERGIES b/test/unittests/cpmd_4.1/md/ntraj/ENERGIES new file mode 100644 index 0000000000000000000000000000000000000000..02c7d2ffbe3c10b2428d26bd946366d011c75922 --- /dev/null +++ b/test/unittests/cpmd_4.1/md/ntraj/ENERGIES @@ -0,0 +1,50 @@ + 1 0.00472945 110.096 -1.1023492072 -1.1018262261 -1.0970967730 0.288545E-05 0.25 + 2 0.01424065 232.496 -1.1128688938 -1.1117644858 -1.0975238350 0.182162E-04 0.26 + 3 0.02228702 351.956 -1.1216882365 -1.1200163669 -1.0977293448 0.596327E-04 0.25 + 4 0.02592222 412.578 -1.1256188624 -1.1236590243 -1.0977368045 0.137607E-03 0.25 + 5 0.02507375 393.180 -1.1245335482 -1.1226658551 -1.0975921059 0.251896E-03 0.41 + 6 0.02170348 311.439 -1.1206087528 -1.1191293469 -1.0974258636 0.389716E-03 0.35 + 7 0.01806912 208.928 -1.1163887071 -1.1153962539 -1.0973271357 0.530786E-03 0.36 + 8 0.01550309 123.508 -1.1133979574 -1.1128112667 -1.0973081718 0.656212E-03 0.37 + 9 0.01428927 71.351 -1.1119610076 -1.1116220739 -1.0973328023 0.755177E-03 0.37 + 10 0.01412005 48.653 -1.1117171754 -1.1114860650 -1.0973660187 0.826435E-03 0.39 + 11 0.01454963 43.205 -1.1121477411 -1.1119425095 -1.0973928823 0.875667E-03 0.33 + 12 0.01522198 44.147 -1.1128400647 -1.1126303571 -1.0974083755 0.911456E-03 0.26 + 13 0.01592316 45.526 -1.1135548344 -1.1133385763 -1.0974154187 0.942258E-03 0.24 + 14 0.01655033 45.568 -1.1141854503 -1.1139689917 -1.0974186637 0.974901E-03 0.24 + 15 0.01706605 44.715 -1.1146975180 -1.1144851121 -1.0974190627 0.101412E-02 0.24 + 16 0.01746680 44.005 -1.1150947618 -1.1148857283 -1.0974189329 0.106282E-02 0.26 + 17 0.01776074 44.244 -1.1153899632 -1.1151797929 -1.0974190575 0.112264E-02 0.35 + 18 0.01795742 45.772 -1.1155935307 -1.1153761050 -1.0974186815 0.119434E-02 0.35 + 19 0.01806576 48.537 -1.1157147808 -1.1154842182 -1.0974184559 0.127815E-02 0.34 + 20 0.01809373 52.255 -1.1157599169 -1.1155116921 -1.0974179583 0.137401E-02 0.32 + 21 0.01805054 56.516 -1.1157360008 -1.1154675379 -1.0974169961 0.148167E-02 0.23 + 22 0.01794636 60.905 -1.1156512292 -1.1153619159 -1.0974155607 0.160074E-02 0.23 + 23 0.01779314 65.074 -1.1155167676 -1.1152076534 -1.0974145094 0.173073E-02 0.23 + 24 0.01760410 68.722 -1.1153426839 -1.1150162383 -1.0974121397 0.187108E-02 0.23 + 25 0.01739640 71.638 -1.1151469827 -1.1148066858 -1.0974102809 0.202107E-02 0.23 + 26 0.01718921 73.709 -1.1149481806 -1.1145980447 -1.0974088338 0.217994E-02 0.23 + 27 0.01699582 74.870 -1.1147573603 -1.1144017101 -1.0974058862 0.234681E-02 0.23 + 28 0.01683495 75.111 -1.1145981234 -1.1142413309 -1.0974063855 0.252070E-02 0.23 + 29 0.01670265 74.489 -1.1144603569 -1.1141065157 -1.0974038654 0.270054E-02 0.22 + 30 0.01661442 73.081 -1.1143644220 -1.1140172732 -1.0974028537 0.288524E-02 0.23 + 31 0.01655815 70.980 -1.1143033888 -1.1139662190 -1.0974080684 0.307358E-02 0.24 + 32 0.01650569 68.325 -1.1142240908 -1.1138995296 -1.0973938363 0.326432E-02 0.22 + 33 0.01657766 65.255 -1.1142857160 -1.1139757411 -1.0973980782 0.345624E-02 0.23 + 34 0.01674936 61.905 -1.1144438592 -1.1141497957 -1.0974004352 0.364807E-02 0.23 + 35 0.01702316 58.440 -1.1146791594 -1.1144015566 -1.0973784004 0.383857E-02 0.22 + 36 0.01763441 55.015 -1.1152782856 -1.1150169543 -1.0973825424 0.402661E-02 0.23 + 37 0.01848514 51.771 -1.1161573098 -1.1159113844 -1.0974262399 0.421112E-02 0.22 + 38 0.01897016 48.857 -1.1166648547 -1.1164327728 -1.0974626172 0.439118E-02 0.22 + 39 0.01858750 46.386 -1.1162605862 -1.1160402423 -1.0974527395 0.456614E-02 0.24 + 40 0.01744917 44.419 -1.1150750202 -1.1148640199 -1.0974148488 0.473558E-02 0.23 + 41 0.01610603 42.978 -1.1136853843 -1.1134812305 -1.0973752036 0.489928E-02 0.23 + 42 0.01516204 42.048 -1.1127114865 -1.1125117498 -1.0973497053 0.505718E-02 0.22 + 43 0.01497724 41.607 -1.1125324644 -1.1123348215 -1.0973575818 0.520925E-02 0.23 + 44 0.01549914 41.655 -1.1130663421 -1.1128684718 -1.0973693342 0.535541E-02 0.23 + 45 0.01649282 42.196 -1.1140950557 -1.1138946136 -1.0974017920 0.549556E-02 0.22 + 46 0.01752242 43.235 -1.1151502868 -1.1149449129 -1.0974224937 0.562968E-02 0.22 + 47 0.01826876 44.768 -1.1159079382 -1.1156952780 -1.0974265218 0.575782E-02 0.23 + 48 0.01863973 46.745 -1.1162911025 -1.1160690555 -1.0974293221 0.588031E-02 0.23 + 49 0.01862430 49.045 -1.1162747263 -1.1160417513 -1.0974174556 0.599772E-02 0.23 + 50 0.01840782 51.542 -1.1160488582 -1.1158040226 -1.0973962069 0.611084E-02 0.22 diff --git a/test/unittests/cpmd_4.1/md/ntraj/GEOMETRY b/test/unittests/cpmd_4.1/md/ntraj/GEOMETRY new file mode 100644 index 0000000000000000000000000000000000000000..99afcdea42b2a843f164962a4b29f8f63c16e0db --- /dev/null +++ b/test/unittests/cpmd_4.1/md/ntraj/GEOMETRY @@ -0,0 +1,2 @@ + 0.740084462274 0.045946600273 0.049790097126 -0.000187193069 0.000212525459 0.000230307582 + -0.740084462274 -0.045946600273 -0.049790097126 0.000187193069 -0.000212525459 -0.000230307582 diff --git a/test/unittests/cpmd_4.1/md/ntraj/GEOMETRY.xyz b/test/unittests/cpmd_4.1/md/ntraj/GEOMETRY.xyz new file mode 100644 index 0000000000000000000000000000000000000000..15b6e3715df41db74f68e973a4f400d438925ea8 --- /dev/null +++ b/test/unittests/cpmd_4.1/md/ntraj/GEOMETRY.xyz @@ -0,0 +1,4 @@ + 2 +GEOMETRY FILE / created by CPMD + H 0.391635831546 0.024313893781 0.026347784726 -0.000099058306 0.000112463630 0.000121873524 + H -0.391635831546 -0.024313893781 -0.026347784726 0.000099058306 -0.000112463630 -0.000121873524 diff --git a/test/unittests/cpmd_4.1/md/ntraj/LATEST b/test/unittests/cpmd_4.1/md/ntraj/LATEST new file mode 100644 index 0000000000000000000000000000000000000000..0e4449210602fd9c3a45bd3bc780cd67ad8721b0 --- /dev/null +++ b/test/unittests/cpmd_4.1/md/ntraj/LATEST @@ -0,0 +1,2 @@ +./RESTART.1 + 1 diff --git a/test/unittests/cpmd_4.1/md/ntraj/RESTART.1 b/test/unittests/cpmd_4.1/md/ntraj/RESTART.1 new file mode 100644 index 0000000000000000000000000000000000000000..f5d79f1aa4969bb60dbcfbca85786c92e0135968 Binary files /dev/null and b/test/unittests/cpmd_4.1/md/ntraj/RESTART.1 differ diff --git a/test/unittests/cpmd_4.1/md/ntraj/TRAJEC.xyz b/test/unittests/cpmd_4.1/md/ntraj/TRAJEC.xyz new file mode 100644 index 0000000000000000000000000000000000000000..d7e893edac3a468b0365fd495885b9e580dc4101 --- /dev/null +++ b/test/unittests/cpmd_4.1/md/ntraj/TRAJEC.xyz @@ -0,0 +1,32 @@ + 2 + STEP: 1 + H 0.371489 0.000511 0.000554 + H -0.371489 -0.000511 -0.000554 + 2 + STEP: 8 + H 0.383197 0.004012 0.004347 + H -0.383197 -0.004012 -0.004347 + 2 + STEP: 15 + H 0.383871 0.007377 0.007994 + H -0.383871 -0.007377 -0.007994 + 2 + STEP: 22 + H 0.384963 0.010793 0.011696 + H -0.384963 -0.010793 -0.011696 + 2 + STEP: 29 + H 0.388694 0.014276 0.015471 + H -0.388694 -0.014276 -0.015471 + 2 + STEP: 36 + H 0.392062 0.017736 0.019220 + H -0.392062 -0.017736 -0.019220 + 2 + STEP: 43 + H 0.393167 0.021093 0.022857 + H -0.393167 -0.021093 -0.022857 + 2 + STEP: 50 + H 0.391636 0.024314 0.026348 + H -0.391636 -0.024314 -0.026348 diff --git a/test/unittests/cpmd_4.1/md/ntraj/TRAJECTORY b/test/unittests/cpmd_4.1/md/ntraj/TRAJECTORY new file mode 100644 index 0000000000000000000000000000000000000000..147fc65673d4ce8634102b0975449d3d083d49b7 --- /dev/null +++ b/test/unittests/cpmd_4.1/md/ntraj/TRAJECTORY @@ -0,0 +1,16 @@ + 1 0.70201340784773 0.00096620207776 0.00104702184853 0.00039772295627 0.00024115257177 0.00026132422738 + 1 -0.70201340784773 -0.00096620207776 -0.00104702184853 -0.00039772295627 -0.00024115257177 -0.00026132422738 + 8 0.72413746922406 0.00758077571951 0.00821488383936 0.00045168695311 0.00023026062676 0.00024952121008 + 8 -0.72413746922405 -0.00758077571951 -0.00821488383936 -0.00045168695311 -0.00023026062676 -0.00024952121008 + 15 0.72541141597952 0.01393987125682 0.01510589837261 -0.00005721545799 0.00022729120928 0.00024630345710 + 15 -0.72541141597952 -0.01393987125682 -0.01510589837261 0.00005721545799 -0.00022729120928 -0.00024630345710 + 22 0.72747394256230 0.02039650999872 0.02210261801843 0.00019672664260 0.00023370463452 0.00025325351120 + 22 -0.72747394256230 -0.02039650999872 -0.02210261801843 -0.00019672664260 -0.00023370463452 -0.00025325351120 + 29 0.73452501168355 0.02697851051064 0.02923519332609 0.00026869648870 0.00023529533309 0.00025497768132 + 29 -0.73452501168355 -0.02697851051064 -0.02923519332609 -0.00026869648870 -0.00023529533309 -0.00025497768132 + 36 0.74089002841595 0.03351605907910 0.03631961522256 0.00016284624701 0.00023068680238 0.00024998447545 + 36 -0.74089002841595 -0.03351605907910 -0.03631961522256 -0.00016284624701 -0.00023068680238 -0.00024998447545 + 43 0.74297731733313 0.03986003838995 0.04319430656967 -0.00001474968690 0.00022219565239 0.00024078445181 + 43 -0.74297731733313 -0.03986003838995 -0.04319430656967 0.00001474968690 -0.00022219565239 -0.00024078445181 + 50 0.74008446227396 0.04594660027294 0.04979009712617 -0.00018719306900 0.00021252545941 0.00023030758250 + 50 -0.74008446227396 -0.04594660027294 -0.04979009712617 0.00018719306900 -0.00021252545941 -0.00023030758250 diff --git a/test/unittests/cpmd_4.1/md/ntraj/input.inp b/test/unittests/cpmd_4.1/md/ntraj/input.inp new file mode 100755 index 0000000000000000000000000000000000000000..f698db9707b03d92a16eb4bfad7997ac29725e68 --- /dev/null +++ b/test/unittests/cpmd_4.1/md/ntraj/input.inp @@ -0,0 +1,42 @@ +&INFO +isolated hydrogen molecule. +simple molecular dynamics deltat=4au +&END + +&CPMD + MOLECULAR DYNAMICS CP + + TRAJECTORY XYZ SAMPLE + 7 + + TEMPERATURE + 50.0D0 + + MAXSTEP + 50 + TIMESTEP + 4.0 +&END + +&SYSTEM + SYMMETRY + 1 + ANGSTROM + CELL + 8.00 1.0 1.0 0.0 0.0 0.0 + CUTOFF + 70.0 +&END + +&DFT + FUNCTIONAL LDA +&END + +&ATOMS +*H_MT_LDA.psp + LMAX=S + 2 + 0.371 0.000 0.000 +-0.371 0.000 0.000 +&END + diff --git a/test/unittests/cpmd_4.1/md/ntraj/output.out b/test/unittests/cpmd_4.1/md/ntraj/output.out new file mode 100644 index 0000000000000000000000000000000000000000..2d7249c527d6940aa47276616a237b15cce566e0 --- /dev/null +++ b/test/unittests/cpmd_4.1/md/ntraj/output.out @@ -0,0 +1,373 @@ + cp_groups: we are using a 1 x 1 grid (groups x nprocs). + PROGRAM CPMD STARTED AT: 2016-07-26 14:08:55.686 + SETCNST| USING: CODATA 2006 UNITS + + + ****** ****** **** **** ****** + ******* ******* ********** ******* + *** ** *** ** **** ** ** *** + ** ** *** ** ** ** ** ** + ** ******* ** ** ** ** + *** ****** ** ** ** *** + ******* ** ** ** ******* + ****** ** ** ** ****** + + VERSION 4.1-rUnversioned directory + + COPYRIGHT + IBM RESEARCH DIVISION + MPI FESTKOERPERFORSCHUNG STUTTGART + + The CPMD consortium + Home Page: http://www.cpmd.org + Mailing List: cpmd-list@cpmd.org + E-mail: cpmd@cpmd.org + + + *** Jun 22 2016 -- 12:41:05 *** + + THE INPUT FILE IS: input.inp + THIS JOB RUNS ON: lenovo700 + THE CURRENT DIRECTORY IS: + /home/lauri/Dropbox/nomad-dev/nomad-lab-base/parsers/cpmd/test/unittests/cpmd_4.1/md/ntraj + THE TEMPORARY DIRECTORY IS: + /home/lauri/Dropbox/nomad-dev/nomad-lab-base/parsers/cpmd/test/unittests/cpmd_4.1/md/ntraj + THE PROCESS ID IS: 10413 + THE JOB WAS SUBMITTED BY: lauri + + + ****************************************************************************** + * INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO * + ****************************************************************************** + * isolated hydrogen molecule. * + * simple molecular dynamics deltat=4au * + ****************************************************************************** + + CAR-PARRINELLO MOLECULAR DYNAMICS + + USING SEED 123456 TO INIT. PSEUDO RANDOM NUMBER GEN. + PATH TO THE RESTART FILES: ./ + ITERATIVE ORTHOGONALIZATION + MAXIT: 30 + EPS: 1.00E-06 + MAXIMUM NUMBER OF STEPS: 50 STEPS + MAXIMUM NUMBER OF ITERATIONS FOR SC: 10000 STEPS + PRINT INTERMEDIATE RESULTS EVERY 10001 STEPS + STORE INTERMEDIATE RESULTS EVERY 10001 STEPS + STORE INTERMEDIATE RESULTS EVERY 10001 SELF-CONSISTENT STEPS + NUMBER OF DISTINCT RESTART FILES: 1 + TEMPERATURE IS CALCULATED ASSUMING EXTENDED BULK BEHAVIOR + FICTITIOUS ELECTRON MASS: 400.0000 + TIME STEP FOR ELECTRONS: 4.0000 + TIME STEP FOR IONS: 4.0000 + TRAJECTORIES ARE SAVED ON FILE EVERY 7 STEPS + TRAJEC.xyz IS SAVED ON FILE EVERY 7 STEPS + ELECTRON DYNAMICS: THE TEMPERATURE IS NOT CONTROLLED + ION DYNAMICS: THE TEMPERATURE IS NOT CONTROLLED + SPLINE INTERPOLATION IN G-SPACE FOR PSEUDOPOTENTIAL FUNCTIONS + NUMBER OF SPLINE POINTS: 5000 + + EXCHANGE CORRELATION FUNCTIONALS + LDA EXCHANGE: NONE + LDA XC THROUGH PADE APPROXIMATION + S.GOEDECKER, J.HUTTER, M.TETER PRB 541703 (1996) + + *** DETSP| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + + ***************************** ATOMS **************************** + NR TYPE X(BOHR) Y(BOHR) Z(BOHR) MBL + 1 H 0.701088 0.000000 0.000000 3 + 2 H -0.701088 0.000000 0.000000 3 + **************************************************************** + + NUMBER OF STATES: 1 + NUMBER OF ELECTRONS: 2.00000 + CHARGE: 0.00000 + ELECTRON TEMPERATURE(KELVIN): 0.00000 + OCCUPATION + 2.0 + + ============================================================ + | Pseudopotential Report Thu Jan 11 18:21:49 1996 | + ------------------------------------------------------------ + | Atomic Symbol : H | + | Atomic Number : 1 | + | Number of core states : 0 | + | Number of valence states : 1 | + | Exchange-Correlation Functional : | + | Slater exchange : .6667 | + | LDA correlation : Ceperley-Alder | + | Electron Configuration : N L Occupation | + | 1 S 1.0000 | + | Full Potential Total Energy -.445894 | + | Trouiller-Martins normconserving PP | + | n l rc energy | + | 1 S .5000 -.23366 | + | 2 P .5000 -.23366 | + | Number of Mesh Points : 511 | + | Pseudoatom Total Energy -.445889 | + ============================================================ + + **************************************************************** + * ATOM MASS RAGGIO NLCC PSEUDOPOTENTIAL * + * H 1.0080 1.2000 NO S LOCAL * + **************************************************************** + + + PARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARA + NCPU NGW NHG PLANES GXRAYS HXRAYS ORBITALS Z-PLANES + 0 17133 136605 90 1281 5089 1 1 + G=0 COMPONENT ON PROCESSOR : 0 + PARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARA + + *** loadpa| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + + OPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPEN + NUMBER OF CPUS PER TASK 1 + OPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPEN + + *** rggen| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + + ************************** SUPERCELL *************************** + SYMMETRY: SIMPLE CUBIC + LATTICE CONSTANT(a.u.): 15.11781 + CELL DIMENSION: 15.1178 1.0000 1.0000 0.0000 0.0000 0.0000 + VOLUME(OMEGA IN BOHR^3): 3455.14726 + LATTICE VECTOR A1(BOHR): 15.1178 0.0000 0.0000 + LATTICE VECTOR A2(BOHR): 0.0000 15.1178 0.0000 + LATTICE VECTOR A3(BOHR): 0.0000 0.0000 15.1178 + RECIP. LAT. VEC. B1(2Pi/BOHR): 0.0661 0.0000 0.0000 + RECIP. LAT. VEC. B2(2Pi/BOHR): 0.0000 0.0661 0.0000 + RECIP. LAT. VEC. B3(2Pi/BOHR): 0.0000 0.0000 0.0661 + REAL SPACE MESH: 90 90 90 + WAVEFUNCTION CUTOFF(RYDBERG): 70.00000 + DENSITY CUTOFF(RYDBERG): (DUAL= 4.00) 280.00000 + NUMBER OF PLANE WAVES FOR WAVEFUNCTION CUTOFF: 17133 + NUMBER OF PLANE WAVES FOR DENSITY CUTOFF: 136605 + **************************************************************** + + *** RINFORCE| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + *** FFTPRP| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + + GENERATE ATOMIC BASIS SET + H SLATER ORBITALS + 1S ALPHA= 1.0000 OCCUPATION= 1.00 + + + INITIALIZATION TIME: 0.48 SECONDS + + *** MDPT| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + *** PHFAC| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + NOTE: ATOMIC GUESS USING DISTRIBUTED LINALG WITH LANCZOS + *** ATOMWF| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + ATRHO| CHARGE(R-SPACE): 2.000000 (G-SPACE): 2.000000 + + **************************************************************** + * ATOMIC COORDINATES * + **************************************************************** + 1 H 0.701088 0.000000 0.000000 + 2 H -0.701088 0.000000 0.000000 + **************************************************************** + + + DEGREES OF FREEDOM FOR SYSTEM: 3 + + RVSCAL| RESCALING IONIC TEMP FROM 50.00000 TO 50.00000 + ================================================================ + == FORCES INITIALIZATION == + ================================================================ + EWALD| SUM IN REAL SPACE OVER 1* 1* 1 CELLS + + **************************************************************** + * ATOMIC COORDINATES * + **************************************************************** + 1 H 0.701088 0.000000 0.000000 + 2 H -0.701088 0.000000 0.000000 + **************************************************************** + + ================================================================ + == END OF FORCES INITIALIZATION == + ================================================================ + + TIME FOR INITIALIZATION: 1.12 SECONDS + + **************************************************************** + * ATOMIC COORDINATES * + **************************************************************** + 1 H 0.702013 0.000966 0.001047 + 2 H -0.702013 -0.000966 -0.001047 + **************************************************************** + + + TOTAL INTEGRATED ELECTRONIC DENSITY + IN G-SPACE = 2.0000000000 + IN R-SPACE = 2.0000000000 + + (K+E1+L+N+X) TOTAL ENERGY = -1.10234921 A.U. + (K) KINETIC ENERGY = 0.83136071 A.U. + (E1=A-S+R) ELECTROSTATIC ENERGY = -0.48680398 A.U. + (S) ESELF = 0.66490380 A.U. + (R) ESR = 0.17235462 A.U. + (L) LOCAL PSEUDOPOTENTIAL ENERGY = -0.86930120 A.U. + (N) N-L PSEUDOPOTENTIAL ENERGY = 0.00000000 A.U. + (X) EXCHANGE-CORRELATION ENERGY = -0.57760473 A.U. + + NFI EKINC TEMPP EKS ECLASSIC EHAM DIS TCPU + 1 0.00473 110.1 -1.10235 -1.10183 -1.09710 0.289E-05 0.25 + 2 0.01424 232.5 -1.11287 -1.11176 -1.09752 0.182E-04 0.26 + 3 0.02229 352.0 -1.12169 -1.12002 -1.09773 0.596E-04 0.25 + 4 0.02592 412.6 -1.12562 -1.12366 -1.09774 0.138E-03 0.25 + 5 0.02507 393.2 -1.12453 -1.12267 -1.09759 0.252E-03 0.41 + 6 0.02170 311.4 -1.12061 -1.11913 -1.09743 0.390E-03 0.35 + 7 0.01807 208.9 -1.11639 -1.11540 -1.09733 0.531E-03 0.36 + 8 0.01550 123.5 -1.11340 -1.11281 -1.09731 0.656E-03 0.37 + 9 0.01429 71.4 -1.11196 -1.11162 -1.09733 0.755E-03 0.37 + 10 0.01412 48.7 -1.11172 -1.11149 -1.09737 0.826E-03 0.39 + 11 0.01455 43.2 -1.11215 -1.11194 -1.09739 0.876E-03 0.33 + 12 0.01522 44.1 -1.11284 -1.11263 -1.09741 0.911E-03 0.26 + 13 0.01592 45.5 -1.11355 -1.11334 -1.09742 0.942E-03 0.24 + 14 0.01655 45.6 -1.11419 -1.11397 -1.09742 0.975E-03 0.24 + 15 0.01707 44.7 -1.11470 -1.11449 -1.09742 0.101E-02 0.24 + 16 0.01747 44.0 -1.11509 -1.11489 -1.09742 0.106E-02 0.26 + 17 0.01776 44.2 -1.11539 -1.11518 -1.09742 0.112E-02 0.35 + 18 0.01796 45.8 -1.11559 -1.11538 -1.09742 0.119E-02 0.35 + 19 0.01807 48.5 -1.11571 -1.11548 -1.09742 0.128E-02 0.34 + 20 0.01809 52.3 -1.11576 -1.11551 -1.09742 0.137E-02 0.32 + 21 0.01805 56.5 -1.11574 -1.11547 -1.09742 0.148E-02 0.23 + 22 0.01795 60.9 -1.11565 -1.11536 -1.09742 0.160E-02 0.23 + 23 0.01779 65.1 -1.11552 -1.11521 -1.09741 0.173E-02 0.23 + 24 0.01760 68.7 -1.11534 -1.11502 -1.09741 0.187E-02 0.23 + 25 0.01740 71.6 -1.11515 -1.11481 -1.09741 0.202E-02 0.23 + 26 0.01719 73.7 -1.11495 -1.11460 -1.09741 0.218E-02 0.23 + 27 0.01700 74.9 -1.11476 -1.11440 -1.09741 0.235E-02 0.23 + 28 0.01683 75.1 -1.11460 -1.11424 -1.09741 0.252E-02 0.23 + 29 0.01670 74.5 -1.11446 -1.11411 -1.09740 0.270E-02 0.22 + 30 0.01661 73.1 -1.11436 -1.11402 -1.09740 0.289E-02 0.23 + 31 0.01656 71.0 -1.11430 -1.11397 -1.09741 0.307E-02 0.24 + 32 0.01651 68.3 -1.11422 -1.11390 -1.09739 0.326E-02 0.22 + 33 0.01658 65.3 -1.11429 -1.11398 -1.09740 0.346E-02 0.23 + 34 0.01675 61.9 -1.11444 -1.11415 -1.09740 0.365E-02 0.23 + 35 0.01702 58.4 -1.11468 -1.11440 -1.09738 0.384E-02 0.22 + 36 0.01763 55.0 -1.11528 -1.11502 -1.09738 0.403E-02 0.23 + 37 0.01849 51.8 -1.11616 -1.11591 -1.09743 0.421E-02 0.22 + 38 0.01897 48.9 -1.11666 -1.11643 -1.09746 0.439E-02 0.22 + 39 0.01859 46.4 -1.11626 -1.11604 -1.09745 0.457E-02 0.24 + 40 0.01745 44.4 -1.11508 -1.11486 -1.09741 0.474E-02 0.23 + 41 0.01611 43.0 -1.11369 -1.11348 -1.09738 0.490E-02 0.23 + 42 0.01516 42.0 -1.11271 -1.11251 -1.09735 0.506E-02 0.22 + 43 0.01498 41.6 -1.11253 -1.11233 -1.09736 0.521E-02 0.23 + 44 0.01550 41.7 -1.11307 -1.11287 -1.09737 0.536E-02 0.23 + 45 0.01649 42.2 -1.11410 -1.11389 -1.09740 0.550E-02 0.22 + 46 0.01752 43.2 -1.11515 -1.11494 -1.09742 0.563E-02 0.22 + 47 0.01827 44.8 -1.11591 -1.11570 -1.09743 0.576E-02 0.23 + 48 0.01864 46.7 -1.11629 -1.11607 -1.09743 0.588E-02 0.23 + 49 0.01862 49.0 -1.11627 -1.11604 -1.09742 0.600E-02 0.23 + 50 0.01841 51.5 -1.11605 -1.11580 -1.09740 0.611E-02 0.22 + + RESTART INFORMATION WRITTEN ON FILE ./RESTART.1 + + **************************************************************** + * AVERAGED QUANTITIES * + **************************************************************** + MEAN VALUE +/- RMS DEVIATION + <x> [<x^2>-<x>^2]**(1/2) + ELECTRON KINETIC ENERGY 0.017239 0.288826E-02 + IONIC TEMPERATURE 88.6689 90.3464 + DENSITY FUNCTIONAL ENERGY -1.115075 0.322126E-02 + CLASSICAL ENERGY -1.114654 0.296260E-02 + CONSERVED ENERGY -1.097415 0.889663E-04 + NOSE ENERGY ELECTRONS 0.000000 0.00000 + NOSE ENERGY IONS 0.000000 0.00000 + CONSTRAINTS ENERGY 0.000000 0.00000 + RESTRAINTS ENERGY 0.000000 0.00000 + ION DISPLACEMENT 0.260644E-02 0.193303E-02 + CPU TIME 0.2600 + + **************************************************************** + * * + * FINAL RESULTS * + * * + **************************************************************** + + **************************************************************** + * ATOMIC COORDINATES * + **************************************************************** + 1 H 0.740084 0.045947 0.049790 + 2 H -0.740084 -0.045947 -0.049790 + **************************************************************** + + + **************************************************************** + + + ELECTRONIC GRADIENT: + MAX. COMPONENT = 1.39929E-02 NORM = 2.08955E-03 + + TOTAL INTEGRATED ELECTRONIC DENSITY + IN G-SPACE = 1.9999999999 + IN R-SPACE = 1.9999999999 + + (K+E1+L+N+X) TOTAL ENERGY = -1.11604886 A.U. + (K) KINETIC ENERGY = 1.06454894 A.U. + (E1=A-S+R) ELECTROSTATIC ENERGY = -0.50409415 A.U. + (S) ESELF = 0.66490380 A.U. + (R) ESR = 0.14497305 A.U. + (L) LOCAL PSEUDOPOTENTIAL ENERGY = -1.04064388 A.U. + (N) N-L PSEUDOPOTENTIAL ENERGY = 0.00000000 A.U. + (X) EXCHANGE-CORRELATION ENERGY = -0.63585977 A.U. + + **************************************************************** + + + + **************************************************************** + * * + * TIMING * + * * + **************************************************************** + SUBROUTINE CALLS SELF TIME TOTAL TIME + AVERAGE MAXIMUM AVERAGE MAXIMUM + cpmd 1 0.00 0.00 14.60 14.60 + mdpt 1 0.00 0.00 14.13 14.13 + mdmain 1 0.01 0.01 14.13 14.13 + forcedr 51 0.00 0.00 13.22 13.22 + forces 51 0.00 0.00 13.22 13.22 + forces_a 51 0.00 0.00 10.36 10.36 + rscpot 51 0.00 0.00 10.36 10.36 + vofrho 52 0.00 0.00 8.82 8.82 + INVFFTN 157 5.48 5.48 5.48 5.48 + VOFRHOB 52 0.27 0.27 5.43 5.43 + VOFRHOA 52 0.12 0.12 3.39 3.39 + FWFFTN 105 3.39 3.39 3.39 3.39 + vpsi 53 0.29 0.29 2.94 2.94 + xcener_new 52 0.21 0.21 2.61 2.61 + mikeu 52 2.39 2.39 2.39 2.39 + rhoofr 51 0.44 0.44 1.88 1.88 + initrun 1 0.00 0.00 0.83 0.83 + rinitwf 1 0.00 0.00 0.83 0.83 + ATOMWF 1 0.00 0.00 0.83 0.83 + potfor 51 0.56 0.56 0.56 0.56 + ATRHO 1 0.36 0.36 0.40 0.40 + ppener 52 0.32 0.32 0.32 0.32 + rinit 1 0.00 0.00 0.26 0.26 + rggen 1 0.01 0.01 0.26 0.26 + loadpa 1 0.01 0.01 0.26 0.26 + EICALC 52 0.19 0.19 0.19 0.19 + RINFORCE 1 0.00 0.00 0.10 0.10 + loadpa_b 1 0.10 0.10 0.10 0.10 + NUMPW 1 0.10 0.10 0.10 0.10 + dist_ksmat 1 0.00 0.00 0.10 0.10 + loadpa_c 1 0.10 0.10 0.10 0.10 + FORMFN 1 0.10 0.10 0.10 0.10 + loadpa_a 1 0.04 0.04 0.04 0.04 + POSUPA 50 0.00 0.00 0.02 0.02 + PHFAC 51 0.02 0.02 0.02 0.02 + ovlap 152 0.01 0.01 0.02 0.02 + RORTOG 50 0.00 0.00 0.02 0.02 + **************************************************************** + + CPU TIME : 0 HOURS 0 MINUTES 14.61 SECONDS + ELAPSED TIME : 0 HOURS 0 MINUTES 14.61 SECONDS + *** CPMD| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + + PROGRAM CPMD ENDED AT: 2016-07-26 14:09:10.292 diff --git a/test/unittests/cpmd_4.1/md/ntraj/run.sh b/test/unittests/cpmd_4.1/md/ntraj/run.sh new file mode 100755 index 0000000000000000000000000000000000000000..74ce0ca5a55a21a25741d586bcf4cb42c8f14590 --- /dev/null +++ b/test/unittests/cpmd_4.1/md/ntraj/run.sh @@ -0,0 +1,3 @@ +export CPMD_PP_LIBRARY_PATH=../../ +export OMP_NUM_THREADS=1 +cpmd41 input.inp > output.out diff --git a/test/unittests/cpmd_4.1/md/nve/ENERGIES b/test/unittests/cpmd_4.1/md/nve/ENERGIES new file mode 100644 index 0000000000000000000000000000000000000000..3779f299b02fbce5ef6fbb2303f56c6cf2d640e7 --- /dev/null +++ b/test/unittests/cpmd_4.1/md/nve/ENERGIES @@ -0,0 +1,50 @@ + 1 0.00472945 110.096 -1.1023492072 -1.1018262261 -1.0970967730 0.288545E-05 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-0.04509397524877 -0.04886613330868 0.00016538618998 -0.00021385628867 -0.00023174930644 + 50 0.74008446227396 0.04594660027294 0.04979009712617 -0.00018719306900 0.00021252545941 0.00023030758250 + 50 -0.74008446227396 -0.04594660027294 -0.04979009712617 0.00018719306900 -0.00021252545941 -0.00023030758250 diff --git a/test/unittests/cpmd_4.1/md/nve/input.inp b/test/unittests/cpmd_4.1/md/nve/input.inp new file mode 100755 index 0000000000000000000000000000000000000000..6fc12e118ffb5d28c1e98e28c0b7eac69d1788e7 --- /dev/null +++ b/test/unittests/cpmd_4.1/md/nve/input.inp @@ -0,0 +1,41 @@ +&INFO +isolated hydrogen molecule. +simple molecular dynamics deltat=4au +&END + +&CPMD + MOLECULAR DYNAMICS CP + + TRAJECTORY XYZ + + TEMPERATURE + 50.0D0 + + MAXSTEP + 50 + TIMESTEP + 4.0 +&END + +&SYSTEM + SYMMETRY + 1 + ANGSTROM + CELL + 8.00 1.0 1.0 0.0 0.0 0.0 + CUTOFF + 70.0 +&END + +&DFT + FUNCTIONAL LDA +&END + +&ATOMS +*H_MT_LDA.psp + LMAX=S + 2 + 0.371 0.000 0.000 +-0.371 0.000 0.000 +&END + diff --git a/test/unittests/cpmd_4.1/md/nve/output.out b/test/unittests/cpmd_4.1/md/nve/output.out new file mode 100644 index 0000000000000000000000000000000000000000..b625a45fff05a02658c881cdd8fe97631662722b --- /dev/null +++ b/test/unittests/cpmd_4.1/md/nve/output.out @@ -0,0 +1,374 @@ + cp_groups: we are using a 1 x 1 grid (groups x nprocs). + PROGRAM CPMD STARTED AT: 2016-07-25 17:12:06.301 + SETCNST| USING: CODATA 2006 UNITS + + + ****** ****** **** **** ****** + ******* ******* ********** ******* + *** ** *** ** **** ** ** *** + ** ** *** ** ** ** ** ** + ** ******* ** ** ** ** + *** ****** ** ** ** *** + ******* ** ** ** ******* + ****** ** ** ** ****** + + VERSION 4.1-rUnversioned directory + + COPYRIGHT + IBM RESEARCH DIVISION + MPI FESTKOERPERFORSCHUNG STUTTGART + + The CPMD consortium + Home Page: http://www.cpmd.org + Mailing List: cpmd-list@cpmd.org + E-mail: cpmd@cpmd.org + + + *** Jun 22 2016 -- 12:41:05 *** + + THE INPUT FILE IS: input.inp + THIS JOB RUNS ON: lenovo700 + THE CURRENT DIRECTORY IS: + /home/lauri/Dropbox/nomad-dev/nomad-lab-base/parsers/cpmd/test/unittests/cpmd_4.1/md/nve + THE TEMPORARY DIRECTORY IS: + /home/lauri/Dropbox/nomad-dev/nomad-lab-base/parsers/cpmd/test/unittests/cpmd_4.1/md/nve + THE PROCESS ID IS: 25046 + THE JOB WAS SUBMITTED BY: lauri + + + ****************************************************************************** + * INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO * + ****************************************************************************** + * isolated hydrogen molecule. * + * simple molecular dynamics deltat=4au * + ****************************************************************************** + + CAR-PARRINELLO MOLECULAR DYNAMICS + + USING SEED 123456 TO INIT. PSEUDO RANDOM NUMBER GEN. + PATH TO THE RESTART FILES: ./ + ITERATIVE ORTHOGONALIZATION + MAXIT: 30 + EPS: 1.00E-06 + MAXIMUM NUMBER OF STEPS: 50 STEPS + MAXIMUM NUMBER OF ITERATIONS FOR SC: 10000 STEPS + PRINT INTERMEDIATE RESULTS EVERY 10001 STEPS + STORE INTERMEDIATE RESULTS EVERY 10001 STEPS + STORE INTERMEDIATE RESULTS EVERY 10001 SELF-CONSISTENT STEPS + NUMBER OF DISTINCT RESTART FILES: 1 + TEMPERATURE IS CALCULATED ASSUMING EXTENDED BULK BEHAVIOR + FICTITIOUS ELECTRON MASS: 400.0000 + TIME STEP FOR ELECTRONS: 4.0000 + TIME STEP FOR IONS: 4.0000 + TRAJECTORIES ARE SAVED ON FILE + TRAJEC.xyz IS SAVED ON FILE + ELECTRON DYNAMICS: THE TEMPERATURE IS NOT CONTROLLED + ION DYNAMICS: THE TEMPERATURE IS NOT CONTROLLED + SPLINE INTERPOLATION IN G-SPACE FOR PSEUDOPOTENTIAL FUNCTIONS + NUMBER OF SPLINE POINTS: 5000 + + EXCHANGE CORRELATION FUNCTIONALS + LDA EXCHANGE: NONE + LDA XC THROUGH PADE APPROXIMATION + S.GOEDECKER, J.HUTTER, M.TETER PRB 541703 (1996) + + *** DETSP| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + + ***************************** ATOMS **************************** + NR TYPE X(BOHR) Y(BOHR) Z(BOHR) MBL + 1 H 0.701088 0.000000 0.000000 3 + 2 H -0.701088 0.000000 0.000000 3 + **************************************************************** + + NUMBER OF STATES: 1 + NUMBER OF ELECTRONS: 2.00000 + CHARGE: 0.00000 + ELECTRON TEMPERATURE(KELVIN): 0.00000 + OCCUPATION + 2.0 + + ============================================================ + | Pseudopotential Report Thu Jan 11 18:21:49 1996 | + ------------------------------------------------------------ + | Atomic Symbol : H | + | Atomic Number : 1 | + | Number of core states : 0 | + | Number of valence states : 1 | + | Exchange-Correlation Functional : | + | Slater exchange : .6667 | + | LDA correlation : Ceperley-Alder | + | Electron Configuration : N L Occupation | + | 1 S 1.0000 | + | Full Potential Total Energy -.445894 | + | Trouiller-Martins normconserving PP | + | n l rc energy | + | 1 S .5000 -.23366 | + | 2 P .5000 -.23366 | + | Number of Mesh Points : 511 | + | Pseudoatom Total Energy -.445889 | + ============================================================ + + **************************************************************** + * ATOM MASS RAGGIO NLCC PSEUDOPOTENTIAL * + * H 1.0080 1.2000 NO S LOCAL * + **************************************************************** + + + PARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARA + NCPU NGW NHG PLANES GXRAYS HXRAYS ORBITALS Z-PLANES + 0 17133 136605 90 1281 5089 1 1 + G=0 COMPONENT ON PROCESSOR : 0 + PARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARA + + *** loadpa| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + + OPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPEN + NUMBER OF CPUS PER TASK 1 + OPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPEN + + *** rggen| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + + ************************** SUPERCELL *************************** + SYMMETRY: SIMPLE CUBIC + LATTICE CONSTANT(a.u.): 15.11781 + CELL DIMENSION: 15.1178 1.0000 1.0000 0.0000 0.0000 0.0000 + VOLUME(OMEGA IN BOHR^3): 3455.14726 + LATTICE VECTOR A1(BOHR): 15.1178 0.0000 0.0000 + LATTICE VECTOR A2(BOHR): 0.0000 15.1178 0.0000 + LATTICE VECTOR A3(BOHR): 0.0000 0.0000 15.1178 + RECIP. LAT. VEC. B1(2Pi/BOHR): 0.0661 0.0000 0.0000 + RECIP. LAT. VEC. B2(2Pi/BOHR): 0.0000 0.0661 0.0000 + RECIP. LAT. VEC. B3(2Pi/BOHR): 0.0000 0.0000 0.0661 + REAL SPACE MESH: 90 90 90 + WAVEFUNCTION CUTOFF(RYDBERG): 70.00000 + DENSITY CUTOFF(RYDBERG): (DUAL= 4.00) 280.00000 + NUMBER OF PLANE WAVES FOR WAVEFUNCTION CUTOFF: 17133 + NUMBER OF PLANE WAVES FOR DENSITY CUTOFF: 136605 + **************************************************************** + + *** RINFORCE| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + *** FFTPRP| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + + GENERATE ATOMIC BASIS SET + H SLATER ORBITALS + 1S ALPHA= 1.0000 OCCUPATION= 1.00 + + + INITIALIZATION TIME: 0.48 SECONDS + + *** MDPT| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + *** PHFAC| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + NOTE: ATOMIC GUESS USING DISTRIBUTED LINALG WITH LANCZOS + *** ATOMWF| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + ATRHO| CHARGE(R-SPACE): 2.000000 (G-SPACE): 2.000000 + + **************************************************************** + * ATOMIC COORDINATES * + **************************************************************** + 1 H 0.701088 0.000000 0.000000 + 2 H -0.701088 0.000000 0.000000 + **************************************************************** + + + DEGREES OF FREEDOM FOR SYSTEM: 3 + + RVSCAL| RESCALING IONIC TEMP FROM 50.00000 TO 50.00000 + ================================================================ + == FORCES INITIALIZATION == + ================================================================ + EWALD| SUM IN REAL SPACE OVER 1* 1* 1 CELLS + + **************************************************************** + * ATOMIC COORDINATES * + **************************************************************** + 1 H 0.701088 0.000000 0.000000 + 2 H -0.701088 0.000000 0.000000 + **************************************************************** + + ================================================================ + == END OF FORCES INITIALIZATION == + ================================================================ + + TIME FOR INITIALIZATION: 1.07 SECONDS + + **************************************************************** + * ATOMIC COORDINATES * + **************************************************************** + 1 H 0.702013 0.000966 0.001047 + 2 H -0.702013 -0.000966 -0.001047 + **************************************************************** + + + TOTAL INTEGRATED ELECTRONIC DENSITY + IN G-SPACE = 2.0000000000 + IN R-SPACE = 2.0000000000 + + (K+E1+L+N+X) TOTAL ENERGY = -1.10234921 A.U. + (K) KINETIC ENERGY = 0.83136071 A.U. + (E1=A-S+R) ELECTROSTATIC ENERGY = -0.48680398 A.U. + (S) ESELF = 0.66490380 A.U. + (R) ESR = 0.17235462 A.U. + (L) LOCAL PSEUDOPOTENTIAL ENERGY = -0.86930120 A.U. + (N) N-L PSEUDOPOTENTIAL ENERGY = 0.00000000 A.U. + (X) EXCHANGE-CORRELATION ENERGY = -0.57760473 A.U. + + NFI EKINC TEMPP EKS ECLASSIC EHAM DIS TCPU + 1 0.00473 110.1 -1.10235 -1.10183 -1.09710 0.289E-05 0.25 + 2 0.01424 232.5 -1.11287 -1.11176 -1.09752 0.182E-04 0.25 + 3 0.02229 352.0 -1.12169 -1.12002 -1.09773 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0.01849 51.8 -1.11616 -1.11591 -1.09743 0.421E-02 0.23 + 38 0.01897 48.9 -1.11666 -1.11643 -1.09746 0.439E-02 0.23 + 39 0.01859 46.4 -1.11626 -1.11604 -1.09745 0.457E-02 0.22 + 40 0.01745 44.4 -1.11508 -1.11486 -1.09741 0.474E-02 0.23 + 41 0.01611 43.0 -1.11369 -1.11348 -1.09738 0.490E-02 0.23 + 42 0.01516 42.0 -1.11271 -1.11251 -1.09735 0.506E-02 0.23 + 43 0.01498 41.6 -1.11253 -1.11233 -1.09736 0.521E-02 0.23 + 44 0.01550 41.7 -1.11307 -1.11287 -1.09737 0.536E-02 0.24 + 45 0.01649 42.2 -1.11410 -1.11389 -1.09740 0.550E-02 0.24 + 46 0.01752 43.2 -1.11515 -1.11494 -1.09742 0.563E-02 0.23 + 47 0.01827 44.8 -1.11591 -1.11570 -1.09743 0.576E-02 0.29 + 48 0.01864 46.7 -1.11629 -1.11607 -1.09743 0.588E-02 0.28 + 49 0.01862 49.0 -1.11627 -1.11604 -1.09742 0.600E-02 0.24 + 50 0.01841 51.5 -1.11605 -1.11580 -1.09740 0.611E-02 0.23 + + RESTART INFORMATION WRITTEN ON FILE ./RESTART.1 + + **************************************************************** + * AVERAGED QUANTITIES * + **************************************************************** + MEAN VALUE +/- RMS DEVIATION + <x> [<x^2>-<x>^2]**(1/2) + ELECTRON KINETIC ENERGY 0.017239 0.288826E-02 + IONIC TEMPERATURE 88.6689 90.3464 + DENSITY FUNCTIONAL ENERGY -1.115075 0.322126E-02 + CLASSICAL ENERGY -1.114654 0.296260E-02 + CONSERVED ENERGY -1.097415 0.889663E-04 + NOSE ENERGY ELECTRONS 0.000000 0.00000 + NOSE ENERGY IONS 0.000000 0.00000 + CONSTRAINTS ENERGY 0.000000 0.00000 + RESTRAINTS ENERGY 0.000000 0.00000 + ION DISPLACEMENT 0.260644E-02 0.193303E-02 + CPU TIME 0.2361 + + **************************************************************** + * * + * FINAL RESULTS * + * * + **************************************************************** + + **************************************************************** + * ATOMIC COORDINATES * + **************************************************************** + 1 H 0.740084 0.045947 0.049790 + 2 H -0.740084 -0.045947 -0.049790 + **************************************************************** + + + **************************************************************** + + + ELECTRONIC GRADIENT: + MAX. COMPONENT = 1.39929E-02 NORM = 2.08955E-03 + + TOTAL INTEGRATED ELECTRONIC DENSITY + IN G-SPACE = 1.9999999999 + IN R-SPACE = 1.9999999999 + + (K+E1+L+N+X) TOTAL ENERGY = -1.11604886 A.U. + (K) KINETIC ENERGY = 1.06454894 A.U. + (E1=A-S+R) ELECTROSTATIC ENERGY = -0.50409415 A.U. + (S) ESELF = 0.66490380 A.U. + (R) ESR = 0.14497305 A.U. + (L) LOCAL PSEUDOPOTENTIAL ENERGY = -1.04064388 A.U. + (N) N-L PSEUDOPOTENTIAL ENERGY = 0.00000000 A.U. + (X) EXCHANGE-CORRELATION ENERGY = -0.63585977 A.U. + + **************************************************************** + + + + **************************************************************** + * * + * TIMING * + * * + **************************************************************** + SUBROUTINE CALLS SELF TIME TOTAL TIME + AVERAGE MAXIMUM AVERAGE MAXIMUM + cpmd 1 0.00 0.00 13.36 13.36 + mdpt 1 0.00 0.00 12.89 12.89 + mdmain 1 0.02 0.02 12.89 12.89 + forcedr 51 0.00 0.00 11.98 11.98 + forces 51 0.00 0.00 11.97 11.97 + forces_a 51 0.00 0.00 9.41 9.41 + rscpot 51 0.00 0.00 9.41 9.41 + vofrho 52 0.00 0.00 8.04 8.04 + VOFRHOB 52 0.21 0.21 5.04 5.04 + INVFFTN 157 5.02 5.02 5.02 5.02 + FWFFTN 105 3.00 3.00 3.00 3.00 + VOFRHOA 52 0.12 0.12 3.00 3.00 + vpsi 53 0.26 0.26 2.65 2.65 + xcener_new 52 0.17 0.17 2.46 2.46 + mikeu 52 2.29 2.29 2.29 2.29 + rhoofr 51 0.39 0.39 1.70 1.70 + initrun 1 0.00 0.00 0.83 0.83 + rinitwf 1 0.00 0.00 0.83 0.83 + ATOMWF 1 0.00 0.00 0.83 0.83 + potfor 51 0.49 0.49 0.49 0.49 + ATRHO 1 0.35 0.35 0.40 0.40 + ppener 52 0.29 0.29 0.29 0.29 + rinit 1 0.00 0.00 0.26 0.26 + rggen 1 0.01 0.01 0.26 0.26 + loadpa 1 0.01 0.01 0.26 0.26 + EICALC 52 0.18 0.18 0.18 0.18 + NUMPW 1 0.10 0.10 0.10 0.10 + dist_ksmat 1 0.00 0.00 0.10 0.10 + RINFORCE 1 0.00 0.00 0.10 0.10 + loadpa_b 1 0.10 0.10 0.10 0.10 + loadpa_c 1 0.10 0.10 0.10 0.10 + FORMFN 1 0.10 0.10 0.10 0.10 + loadpa_a 1 0.05 0.05 0.05 0.05 + POSUPA 50 0.01 0.01 0.03 0.03 + ovlap 152 0.01 0.01 0.02 0.02 + VELUPA 100 0.02 0.02 0.02 0.02 + PHFAC 51 0.01 0.01 0.01 0.01 + RORTOG 50 0.00 0.00 0.01 0.01 + **************************************************************** + + CPU TIME : 0 HOURS 0 MINUTES 13.36 SECONDS + ELAPSED TIME : 0 HOURS 0 MINUTES 13.37 SECONDS + *** CPMD| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + + PROGRAM CPMD ENDED AT: 2016-07-25 17:12:19.667 diff --git a/test/unittests/cpmd_4.1/md/nve/run.sh b/test/unittests/cpmd_4.1/md/nve/run.sh new file mode 100755 index 0000000000000000000000000000000000000000..74ce0ca5a55a21a25741d586bcf4cb42c8f14590 --- /dev/null +++ b/test/unittests/cpmd_4.1/md/nve/run.sh @@ -0,0 +1,3 @@ +export CPMD_PP_LIBRARY_PATH=../../ +export OMP_NUM_THREADS=1 +cpmd41 input.inp > output.out diff --git a/test/unittests/cpmd_4.1/md/range/ENERGIES b/test/unittests/cpmd_4.1/md/range/ENERGIES new file mode 100644 index 0000000000000000000000000000000000000000..66527e259ee4971fda2affb0f5b88d45f9305c62 --- /dev/null +++ b/test/unittests/cpmd_4.1/md/range/ENERGIES @@ -0,0 +1,50 @@ + 1 0.00472945 110.096 -1.1023492072 -1.1018262261 -1.0970967730 0.288545E-05 0.24 + 2 0.01424065 232.496 -1.1128688938 -1.1117644858 -1.0975238350 0.182162E-04 0.26 + 3 0.02228702 351.956 -1.1216882365 -1.1200163669 -1.0977293448 0.596327E-04 0.24 + 4 0.02592222 412.578 -1.1256188624 -1.1236590243 -1.0977368045 0.137607E-03 0.24 + 5 0.02507375 393.180 -1.1245335482 -1.1226658551 -1.0975921059 0.251896E-03 0.23 + 6 0.02170348 311.439 -1.1206087528 -1.1191293469 -1.0974258636 0.389716E-03 0.23 + 7 0.01806912 208.928 -1.1163887071 -1.1153962539 -1.0973271357 0.530786E-03 0.23 + 8 0.01550309 123.508 -1.1133979574 -1.1128112667 -1.0973081718 0.656212E-03 0.22 + 9 0.01428927 71.351 -1.1119610076 -1.1116220739 -1.0973328023 0.755177E-03 0.24 + 10 0.01412005 48.653 -1.1117171754 -1.1114860650 -1.0973660187 0.826435E-03 0.23 + 11 0.01454963 43.205 -1.1121477411 -1.1119425095 -1.0973928823 0.875667E-03 0.23 + 12 0.01522198 44.147 -1.1128400647 -1.1126303571 -1.0974083755 0.911456E-03 0.23 + 13 0.01592316 45.526 -1.1135548344 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-1.1160417513 -1.0974174556 0.599772E-02 0.23 + 50 0.01840782 51.542 -1.1160488582 -1.1158040226 -1.0973962069 0.611084E-02 0.23 diff --git a/test/unittests/cpmd_4.1/md/range/GEOMETRY b/test/unittests/cpmd_4.1/md/range/GEOMETRY new file mode 100644 index 0000000000000000000000000000000000000000..99afcdea42b2a843f164962a4b29f8f63c16e0db --- /dev/null +++ b/test/unittests/cpmd_4.1/md/range/GEOMETRY @@ -0,0 +1,2 @@ + 0.740084462274 0.045946600273 0.049790097126 -0.000187193069 0.000212525459 0.000230307582 + -0.740084462274 -0.045946600273 -0.049790097126 0.000187193069 -0.000212525459 -0.000230307582 diff --git a/test/unittests/cpmd_4.1/md/range/GEOMETRY.xyz b/test/unittests/cpmd_4.1/md/range/GEOMETRY.xyz new file mode 100644 index 0000000000000000000000000000000000000000..15b6e3715df41db74f68e973a4f400d438925ea8 --- /dev/null +++ b/test/unittests/cpmd_4.1/md/range/GEOMETRY.xyz @@ -0,0 +1,4 @@ + 2 +GEOMETRY FILE / created by CPMD + H 0.391635831546 0.024313893781 0.026347784726 -0.000099058306 0.000112463630 0.000121873524 + H -0.391635831546 -0.024313893781 -0.026347784726 0.000099058306 -0.000112463630 -0.000121873524 diff --git a/test/unittests/cpmd_4.1/md/range/LATEST b/test/unittests/cpmd_4.1/md/range/LATEST new file mode 100644 index 0000000000000000000000000000000000000000..0e4449210602fd9c3a45bd3bc780cd67ad8721b0 --- /dev/null +++ b/test/unittests/cpmd_4.1/md/range/LATEST @@ -0,0 +1,2 @@ +./RESTART.1 + 1 diff --git a/test/unittests/cpmd_4.1/md/range/RESTART.1 b/test/unittests/cpmd_4.1/md/range/RESTART.1 new file mode 100644 index 0000000000000000000000000000000000000000..2936a0715180dfde3899160f87fd3d7b863c6d64 Binary files /dev/null and b/test/unittests/cpmd_4.1/md/range/RESTART.1 differ diff --git a/test/unittests/cpmd_4.1/md/range/TRAJEC.xyz b/test/unittests/cpmd_4.1/md/range/TRAJEC.xyz new file mode 100644 index 0000000000000000000000000000000000000000..a550acbe47e5c4d4cdbabaf65041ca6e70a0fa95 --- /dev/null +++ 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-0.018223 -0.019747 + 2 + STEP: 38 + H 0.392649 0.018708 0.020273 + H -0.392649 -0.018708 -0.020273 + 2 + STEP: 39 + H 0.392862 0.019190 0.020795 + H -0.392862 -0.019190 -0.020795 + 2 + STEP: 40 + H 0.393019 0.019670 0.021315 + H -0.393019 -0.019670 -0.021315 + 2 + STEP: 41 + H 0.393122 0.020147 0.021832 + H -0.393122 -0.020147 -0.021832 + 2 + STEP: 42 + H 0.393171 0.020621 0.022346 + H -0.393171 -0.020621 -0.022346 + 2 + STEP: 43 + H 0.393167 0.021093 0.022857 + H -0.393167 -0.021093 -0.022857 + 2 + STEP: 44 + H 0.393109 0.021562 0.023366 + H -0.393109 -0.021562 -0.023366 + 2 + STEP: 45 + H 0.392997 0.022028 0.023871 + H -0.392997 -0.022028 -0.023871 + 2 + STEP: 46 + H 0.392831 0.022491 0.024373 + H -0.392831 -0.022491 -0.024373 + 2 + STEP: 47 + H 0.392610 0.022951 0.024871 + H -0.392610 -0.022951 -0.024871 + 2 + STEP: 48 + H 0.392336 0.023409 0.025367 + H -0.392336 -0.023409 -0.025367 + 2 + STEP: 49 + H 0.392010 0.023863 0.025859 + H -0.392010 -0.023863 -0.025859 + 2 + STEP: 50 + H 0.391636 0.024314 0.026348 + H -0.391636 -0.024314 -0.026348 diff --git a/test/unittests/cpmd_4.1/md/range/TRAJECTORY b/test/unittests/cpmd_4.1/md/range/TRAJECTORY new file mode 100644 index 0000000000000000000000000000000000000000..4a0b27c83a61ed24297d986a6125b78fa403fbf7 --- /dev/null +++ b/test/unittests/cpmd_4.1/md/range/TRAJECTORY @@ -0,0 +1,50 @@ + 1 0.70201340784773 0.00096620207776 0.00104702184853 0.00039772295627 0.00024115257177 0.00026132422738 + 2 0.70427017594465 0.00192922057414 0.00209059381907 0.00068971096691 0.00024011990909 0.00026020518573 + 3 0.70753109558303 0.00288716135048 0.00312866333435 0.00088653459833 0.00023876982089 0.00025874216695 + 4 0.71136245273128 0.00383937914123 0.00416053115468 0.00097170700396 0.00023727594271 0.00025712333073 + 5 0.71530475161473 0.00478536889215 0.00518564998016 0.00094644268934 0.00023563385430 0.00025534388718 + 6 0.71893399424602 0.00572444997561 0.00620328225215 0.00082839676152 0.00023386099777 0.00025342273759 + 7 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+1,42 @@ +&INFO +isolated hydrogen molecule. +simple molecular dynamics deltat=4au +&END + +&CPMD + MOLECULAR DYNAMICS CP + + TRAJECTORY XYZ RANGE + 1 1 + + TEMPERATURE + 50.0D0 + + MAXSTEP + 50 + TIMESTEP + 4.0 +&END + +&SYSTEM + SYMMETRY + 1 + ANGSTROM + CELL + 8.00 1.0 1.0 0.0 0.0 0.0 + CUTOFF + 70.0 +&END + +&DFT + FUNCTIONAL LDA +&END + +&ATOMS +*H_MT_LDA.psp + LMAX=S + 2 + 0.371 0.000 0.000 +-0.371 0.000 0.000 +&END + diff --git a/test/unittests/cpmd_4.1/md/range/output.out b/test/unittests/cpmd_4.1/md/range/output.out new file mode 100644 index 0000000000000000000000000000000000000000..d9f7f17e29a6c20ac1e9ab1f1af97fca1b4930c8 --- /dev/null +++ b/test/unittests/cpmd_4.1/md/range/output.out @@ -0,0 +1,374 @@ + cp_groups: we are using a 1 x 1 grid (groups x nprocs). + PROGRAM CPMD STARTED AT: 2016-07-26 14:28:14.740 + SETCNST| USING: CODATA 2006 UNITS + + + ****** ****** **** **** ****** + ******* ******* ********** ******* + *** ** *** ** **** ** ** *** + ** ** *** ** ** ** ** ** + ** ******* ** ** ** ** + *** ****** ** ** ** *** + ******* ** ** ** ******* + ****** ** ** ** ****** + + VERSION 4.1-rUnversioned directory + + COPYRIGHT + IBM RESEARCH DIVISION + MPI FESTKOERPERFORSCHUNG STUTTGART + + The CPMD consortium + Home Page: http://www.cpmd.org + Mailing List: cpmd-list@cpmd.org + E-mail: cpmd@cpmd.org + + + *** Jun 22 2016 -- 12:41:05 *** + + THE INPUT FILE IS: input.inp + THIS JOB RUNS ON: lenovo700 + THE CURRENT DIRECTORY IS: + /home/lauri/Dropbox/nomad-dev/nomad-lab-base/parsers/cpmd/test/unittests/cpmd_4.1/md/range + THE TEMPORARY DIRECTORY IS: + /home/lauri/Dropbox/nomad-dev/nomad-lab-base/parsers/cpmd/test/unittests/cpmd_4.1/md/range + THE PROCESS ID IS: 11976 + THE JOB WAS SUBMITTED BY: lauri + + + ****************************************************************************** + * INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO * + ****************************************************************************** + * isolated hydrogen molecule. * + * simple molecular dynamics deltat=4au * + ****************************************************************************** + + CAR-PARRINELLO MOLECULAR DYNAMICS + + USING SEED 123456 TO INIT. PSEUDO RANDOM NUMBER GEN. + PATH TO THE RESTART FILES: ./ + ITERATIVE ORTHOGONALIZATION + MAXIT: 30 + EPS: 1.00E-06 + MAXIMUM NUMBER OF STEPS: 50 STEPS + MAXIMUM NUMBER OF ITERATIONS FOR SC: 10000 STEPS + PRINT INTERMEDIATE RESULTS EVERY 10001 STEPS + STORE INTERMEDIATE RESULTS EVERY 10001 STEPS + STORE INTERMEDIATE RESULTS EVERY 10001 SELF-CONSISTENT STEPS + NUMBER OF DISTINCT RESTART FILES: 1 + TEMPERATURE IS CALCULATED ASSUMING EXTENDED BULK BEHAVIOR + FICTITIOUS ELECTRON MASS: 400.0000 + TIME STEP FOR ELECTRONS: 4.0000 + TIME STEP FOR IONS: 4.0000 + TRAJECTORIES ARE SAVED ON FILE + TRAJEC.xyz IS SAVED ON FILE + ELECTRON DYNAMICS: THE TEMPERATURE IS NOT CONTROLLED + ION DYNAMICS: THE TEMPERATURE IS NOT CONTROLLED + SPLINE INTERPOLATION IN G-SPACE FOR PSEUDOPOTENTIAL FUNCTIONS + NUMBER OF SPLINE POINTS: 5000 + + EXCHANGE CORRELATION FUNCTIONALS + LDA EXCHANGE: NONE + LDA XC THROUGH PADE APPROXIMATION + S.GOEDECKER, J.HUTTER, M.TETER PRB 541703 (1996) + + *** DETSP| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + + ***************************** ATOMS **************************** + NR TYPE X(BOHR) Y(BOHR) Z(BOHR) MBL + 1 H 0.701088 0.000000 0.000000 3 + 2 H -0.701088 0.000000 0.000000 3 + **************************************************************** + + NUMBER OF STATES: 1 + NUMBER OF ELECTRONS: 2.00000 + CHARGE: 0.00000 + ELECTRON TEMPERATURE(KELVIN): 0.00000 + OCCUPATION + 2.0 + + ============================================================ + | Pseudopotential Report Thu Jan 11 18:21:49 1996 | + ------------------------------------------------------------ + | Atomic Symbol : H | + | Atomic Number : 1 | + | Number of core states : 0 | + | Number of valence states : 1 | + | Exchange-Correlation Functional : | + | Slater exchange : .6667 | + | LDA correlation : Ceperley-Alder | + | Electron Configuration : N L Occupation | + | 1 S 1.0000 | + | Full Potential Total Energy -.445894 | + | Trouiller-Martins normconserving PP | + | n l rc energy | + | 1 S .5000 -.23366 | + | 2 P .5000 -.23366 | + | Number of Mesh Points : 511 | + | Pseudoatom Total Energy -.445889 | + ============================================================ + + **************************************************************** + * ATOM MASS RAGGIO NLCC PSEUDOPOTENTIAL * + * H 1.0080 1.2000 NO S LOCAL * + **************************************************************** + + + PARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARA + NCPU NGW NHG PLANES GXRAYS HXRAYS ORBITALS Z-PLANES + 0 17133 136605 90 1281 5089 1 1 + G=0 COMPONENT ON PROCESSOR : 0 + PARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARA + + *** loadpa| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + + OPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPEN + NUMBER OF CPUS PER TASK 1 + OPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPEN + + *** rggen| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + + ************************** SUPERCELL *************************** + SYMMETRY: SIMPLE CUBIC + LATTICE CONSTANT(a.u.): 15.11781 + CELL DIMENSION: 15.1178 1.0000 1.0000 0.0000 0.0000 0.0000 + VOLUME(OMEGA IN BOHR^3): 3455.14726 + LATTICE VECTOR A1(BOHR): 15.1178 0.0000 0.0000 + LATTICE VECTOR A2(BOHR): 0.0000 15.1178 0.0000 + LATTICE VECTOR A3(BOHR): 0.0000 0.0000 15.1178 + RECIP. LAT. VEC. B1(2Pi/BOHR): 0.0661 0.0000 0.0000 + RECIP. LAT. VEC. B2(2Pi/BOHR): 0.0000 0.0661 0.0000 + RECIP. LAT. VEC. B3(2Pi/BOHR): 0.0000 0.0000 0.0661 + REAL SPACE MESH: 90 90 90 + WAVEFUNCTION CUTOFF(RYDBERG): 70.00000 + DENSITY CUTOFF(RYDBERG): (DUAL= 4.00) 280.00000 + NUMBER OF PLANE WAVES FOR WAVEFUNCTION CUTOFF: 17133 + NUMBER OF PLANE WAVES FOR DENSITY CUTOFF: 136605 + **************************************************************** + + *** RINFORCE| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + *** FFTPRP| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + + GENERATE ATOMIC BASIS SET + H SLATER ORBITALS + 1S ALPHA= 1.0000 OCCUPATION= 1.00 + + + INITIALIZATION TIME: 0.48 SECONDS + + *** MDPT| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + *** PHFAC| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + NOTE: ATOMIC GUESS USING DISTRIBUTED LINALG WITH LANCZOS + *** ATOMWF| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + ATRHO| CHARGE(R-SPACE): 2.000000 (G-SPACE): 2.000000 + + **************************************************************** + * ATOMIC COORDINATES * + **************************************************************** + 1 H 0.701088 0.000000 0.000000 + 2 H -0.701088 0.000000 0.000000 + **************************************************************** + + + DEGREES OF FREEDOM FOR SYSTEM: 3 + + RVSCAL| RESCALING IONIC TEMP FROM 50.00000 TO 50.00000 + ================================================================ + == FORCES INITIALIZATION == + ================================================================ + EWALD| SUM IN REAL SPACE OVER 1* 1* 1 CELLS + + **************************************************************** + * ATOMIC COORDINATES * + **************************************************************** + 1 H 0.701088 0.000000 0.000000 + 2 H -0.701088 0.000000 0.000000 + **************************************************************** + + ================================================================ + == END OF FORCES INITIALIZATION == + ================================================================ + + TIME FOR INITIALIZATION: 1.06 SECONDS + + **************************************************************** + * ATOMIC COORDINATES * + **************************************************************** + 1 H 0.702013 0.000966 0.001047 + 2 H -0.702013 -0.000966 -0.001047 + **************************************************************** + + + TOTAL INTEGRATED ELECTRONIC DENSITY + IN G-SPACE = 2.0000000000 + IN R-SPACE = 2.0000000000 + + (K+E1+L+N+X) TOTAL ENERGY = -1.10234921 A.U. + (K) KINETIC ENERGY = 0.83136071 A.U. + (E1=A-S+R) ELECTROSTATIC ENERGY = -0.48680398 A.U. + (S) ESELF = 0.66490380 A.U. + (R) ESR = 0.17235462 A.U. + (L) LOCAL PSEUDOPOTENTIAL ENERGY = -0.86930120 A.U. + (N) N-L PSEUDOPOTENTIAL ENERGY = 0.00000000 A.U. + (X) EXCHANGE-CORRELATION ENERGY = -0.57760473 A.U. + + NFI EKINC TEMPP EKS ECLASSIC EHAM DIS TCPU + 1 0.00473 110.1 -1.10235 -1.10183 -1.09710 0.289E-05 0.24 + 2 0.01424 232.5 -1.11287 -1.11176 -1.09752 0.182E-04 0.26 + 3 0.02229 352.0 -1.12169 -1.12002 -1.09773 0.596E-04 0.24 + 4 0.02592 412.6 -1.12562 -1.12366 -1.09774 0.138E-03 0.24 + 5 0.02507 393.2 -1.12453 -1.12267 -1.09759 0.252E-03 0.23 + 6 0.02170 311.4 -1.12061 -1.11913 -1.09743 0.390E-03 0.23 + 7 0.01807 208.9 -1.11639 -1.11540 -1.09733 0.531E-03 0.23 + 8 0.01550 123.5 -1.11340 -1.11281 -1.09731 0.656E-03 0.22 + 9 0.01429 71.4 -1.11196 -1.11162 -1.09733 0.755E-03 0.24 + 10 0.01412 48.7 -1.11172 -1.11149 -1.09737 0.826E-03 0.23 + 11 0.01455 43.2 -1.11215 -1.11194 -1.09739 0.876E-03 0.23 + 12 0.01522 44.1 -1.11284 -1.11263 -1.09741 0.911E-03 0.23 + 13 0.01592 45.5 -1.11355 -1.11334 -1.09742 0.942E-03 0.26 + 14 0.01655 45.6 -1.11419 -1.11397 -1.09742 0.975E-03 0.31 + 15 0.01707 44.7 -1.11470 -1.11449 -1.09742 0.101E-02 0.32 + 16 0.01747 44.0 -1.11509 -1.11489 -1.09742 0.106E-02 0.31 + 17 0.01776 44.2 -1.11539 -1.11518 -1.09742 0.112E-02 0.24 + 18 0.01796 45.8 -1.11559 -1.11538 -1.09742 0.119E-02 0.23 + 19 0.01807 48.5 -1.11571 -1.11548 -1.09742 0.128E-02 0.24 + 20 0.01809 52.3 -1.11576 -1.11551 -1.09742 0.137E-02 0.23 + 21 0.01805 56.5 -1.11574 -1.11547 -1.09742 0.148E-02 0.30 + 22 0.01795 60.9 -1.11565 -1.11536 -1.09742 0.160E-02 0.30 + 23 0.01779 65.1 -1.11552 -1.11521 -1.09741 0.173E-02 0.31 + 24 0.01760 68.7 -1.11534 -1.11502 -1.09741 0.187E-02 0.28 + 25 0.01740 71.6 -1.11515 -1.11481 -1.09741 0.202E-02 0.23 + 26 0.01719 73.7 -1.11495 -1.11460 -1.09741 0.218E-02 0.24 + 27 0.01700 74.9 -1.11476 -1.11440 -1.09741 0.235E-02 0.24 + 28 0.01683 75.1 -1.11460 -1.11424 -1.09741 0.252E-02 0.24 + 29 0.01670 74.5 -1.11446 -1.11411 -1.09740 0.270E-02 0.24 + 30 0.01661 73.1 -1.11436 -1.11402 -1.09740 0.289E-02 0.24 + 31 0.01656 71.0 -1.11430 -1.11397 -1.09741 0.307E-02 0.23 + 32 0.01651 68.3 -1.11422 -1.11390 -1.09739 0.326E-02 0.23 + 33 0.01658 65.3 -1.11429 -1.11398 -1.09740 0.346E-02 0.22 + 34 0.01675 61.9 -1.11444 -1.11415 -1.09740 0.365E-02 0.23 + 35 0.01702 58.4 -1.11468 -1.11440 -1.09738 0.384E-02 0.22 + 36 0.01763 55.0 -1.11528 -1.11502 -1.09738 0.403E-02 0.22 + 37 0.01849 51.8 -1.11616 -1.11591 -1.09743 0.421E-02 0.23 + 38 0.01897 48.9 -1.11666 -1.11643 -1.09746 0.439E-02 0.23 + 39 0.01859 46.4 -1.11626 -1.11604 -1.09745 0.457E-02 0.22 + 40 0.01745 44.4 -1.11508 -1.11486 -1.09741 0.474E-02 0.23 + 41 0.01611 43.0 -1.11369 -1.11348 -1.09738 0.490E-02 0.23 + 42 0.01516 42.0 -1.11271 -1.11251 -1.09735 0.506E-02 0.23 + 43 0.01498 41.6 -1.11253 -1.11233 -1.09736 0.521E-02 0.23 + 44 0.01550 41.7 -1.11307 -1.11287 -1.09737 0.536E-02 0.23 + 45 0.01649 42.2 -1.11410 -1.11389 -1.09740 0.550E-02 0.23 + 46 0.01752 43.2 -1.11515 -1.11494 -1.09742 0.563E-02 0.23 + 47 0.01827 44.8 -1.11591 -1.11570 -1.09743 0.576E-02 0.24 + 48 0.01864 46.7 -1.11629 -1.11607 -1.09743 0.588E-02 0.24 + 49 0.01862 49.0 -1.11627 -1.11604 -1.09742 0.600E-02 0.23 + 50 0.01841 51.5 -1.11605 -1.11580 -1.09740 0.611E-02 0.23 + + RESTART INFORMATION WRITTEN ON FILE ./RESTART.1 + + **************************************************************** + * AVERAGED QUANTITIES * + **************************************************************** + MEAN VALUE +/- RMS DEVIATION + <x> [<x^2>-<x>^2]**(1/2) + ELECTRON KINETIC ENERGY 0.017239 0.288826E-02 + IONIC TEMPERATURE 88.6689 90.3464 + DENSITY FUNCTIONAL ENERGY -1.115075 0.322126E-02 + CLASSICAL ENERGY -1.114654 0.296260E-02 + CONSERVED ENERGY -1.097415 0.889663E-04 + NOSE ENERGY ELECTRONS 0.000000 0.00000 + NOSE ENERGY IONS 0.000000 0.00000 + CONSTRAINTS ENERGY 0.000000 0.00000 + RESTRAINTS ENERGY 0.000000 0.00000 + ION DISPLACEMENT 0.260644E-02 0.193303E-02 + CPU TIME 0.2417 + + **************************************************************** + * * + * FINAL RESULTS * + * * + **************************************************************** + + **************************************************************** + * ATOMIC COORDINATES * + **************************************************************** + 1 H 0.740084 0.045947 0.049790 + 2 H -0.740084 -0.045947 -0.049790 + **************************************************************** + + + **************************************************************** + + + ELECTRONIC GRADIENT: + MAX. COMPONENT = 1.39929E-02 NORM = 2.08955E-03 + + TOTAL INTEGRATED ELECTRONIC DENSITY + IN G-SPACE = 1.9999999999 + IN R-SPACE = 1.9999999999 + + (K+E1+L+N+X) TOTAL ENERGY = -1.11604886 A.U. + (K) KINETIC ENERGY = 1.06454894 A.U. + (E1=A-S+R) ELECTROSTATIC ENERGY = -0.50409415 A.U. + (S) ESELF = 0.66490380 A.U. + (R) ESR = 0.14497305 A.U. + (L) LOCAL PSEUDOPOTENTIAL ENERGY = -1.04064388 A.U. + (N) N-L PSEUDOPOTENTIAL ENERGY = 0.00000000 A.U. + (X) EXCHANGE-CORRELATION ENERGY = -0.63585977 A.U. + + **************************************************************** + + + + **************************************************************** + * * + * TIMING * + * * + **************************************************************** + SUBROUTINE CALLS SELF TIME TOTAL TIME + AVERAGE MAXIMUM AVERAGE MAXIMUM + cpmd 1 0.00 0.00 13.62 13.62 + mdpt 1 0.00 0.00 13.15 13.15 + mdmain 1 0.02 0.02 13.15 13.15 + forcedr 51 0.00 0.00 12.24 12.24 + forces 51 0.00 0.00 12.24 12.24 + forces_a 51 0.00 0.00 9.59 9.59 + rscpot 51 0.00 0.00 9.59 9.59 + vofrho 52 0.00 0.00 8.17 8.17 + INVFFTN 157 5.11 5.11 5.11 5.11 + VOFRHOB 52 0.21 0.21 5.10 5.10 + FWFFTN 105 3.12 3.12 3.12 3.12 + VOFRHOA 52 0.12 0.12 3.07 3.07 + vpsi 53 0.28 0.28 2.75 2.75 + xcener_new 52 0.19 0.19 2.50 2.50 + mikeu 52 2.31 2.31 2.31 2.31 + rhoofr 51 0.39 0.39 1.73 1.73 + initrun 1 0.00 0.00 0.82 0.82 + rinitwf 1 0.00 0.00 0.82 0.82 + ATOMWF 1 0.00 0.00 0.82 0.82 + potfor 51 0.48 0.48 0.48 0.48 + ATRHO 1 0.35 0.35 0.40 0.40 + ppener 52 0.30 0.30 0.30 0.30 + rinit 1 0.00 0.00 0.26 0.26 + rggen 1 0.01 0.01 0.26 0.26 + loadpa 1 0.01 0.01 0.25 0.25 + EICALC 52 0.18 0.18 0.18 0.18 + dist_ksmat 1 0.00 0.00 0.11 0.11 + RINFORCE 1 0.00 0.00 0.10 0.10 + NUMPW 1 0.10 0.10 0.10 0.10 + loadpa_b 1 0.10 0.10 0.10 0.10 + FORMFN 1 0.10 0.10 0.10 0.10 + loadpa_c 1 0.10 0.10 0.10 0.10 + loadpa_a 1 0.04 0.04 0.04 0.04 + POSUPA 50 0.01 0.01 0.03 0.03 + ROTATE 152 0.02 0.02 0.02 0.02 + ovlap 152 0.01 0.01 0.02 0.02 + RORTOG 50 0.00 0.00 0.02 0.02 + PHFAC 51 0.01 0.01 0.01 0.01 + **************************************************************** + + CPU TIME : 0 HOURS 0 MINUTES 13.63 SECONDS + ELAPSED TIME : 0 HOURS 0 MINUTES 13.63 SECONDS + *** CPMD| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + + PROGRAM CPMD ENDED AT: 2016-07-26 14:28:28.366 diff --git a/test/unittests/cpmd_4.1/md/range/run.sh b/test/unittests/cpmd_4.1/md/range/run.sh new file mode 100755 index 0000000000000000000000000000000000000000..74ce0ca5a55a21a25741d586bcf4cb42c8f14590 --- /dev/null +++ b/test/unittests/cpmd_4.1/md/range/run.sh @@ -0,0 +1,3 @@ +export CPMD_PP_LIBRARY_PATH=../../ +export OMP_NUM_THREADS=1 +cpmd41 input.inp > output.out diff --git a/test/unittests/cpmd_4.1/md/xyz/input.inp b/test/unittests/cpmd_4.1/md/xyz/input.inp new file mode 100755 index 0000000000000000000000000000000000000000..6fc12e118ffb5d28c1e98e28c0b7eac69d1788e7 --- /dev/null +++ b/test/unittests/cpmd_4.1/md/xyz/input.inp @@ -0,0 +1,41 @@ +&INFO +isolated hydrogen molecule. +simple molecular dynamics deltat=4au +&END + +&CPMD + MOLECULAR DYNAMICS CP + + TRAJECTORY XYZ + + TEMPERATURE + 50.0D0 + + MAXSTEP + 50 + TIMESTEP + 4.0 +&END + +&SYSTEM + SYMMETRY + 1 + ANGSTROM + CELL + 8.00 1.0 1.0 0.0 0.0 0.0 + CUTOFF + 70.0 +&END + +&DFT + FUNCTIONAL LDA +&END + +&ATOMS +*H_MT_LDA.psp + LMAX=S + 2 + 0.371 0.000 0.000 +-0.371 0.000 0.000 +&END + diff --git a/test/unittests/cpmd_4.1/md/xyz/run.sh b/test/unittests/cpmd_4.1/md/xyz/run.sh new file mode 100755 index 0000000000000000000000000000000000000000..74ce0ca5a55a21a25741d586bcf4cb42c8f14590 --- /dev/null +++ b/test/unittests/cpmd_4.1/md/xyz/run.sh @@ -0,0 +1,3 @@ +export CPMD_PP_LIBRARY_PATH=../../ +export OMP_NUM_THREADS=1 +cpmd41 input.inp > output.out diff --git a/test/unittests/cpmd_4.1/run_tests.py b/test/unittests/cpmd_4.1/run_tests.py index da888cf26ee23c761e83f95b05c859752a34818b..15bc9ee91799f44d4fe3b49b031cc849ed15ab6c 100644 --- a/test/unittests/cpmd_4.1/run_tests.py +++ b/test/unittests/cpmd_4.1/run_tests.py @@ -377,6 +377,198 @@ class TestGeoOpt(unittest.TestCase): self.assertTrue(np.array_equal(result, expected_result)) +#=============================================================================== +class TestMD(unittest.TestCase): + + @classmethod + def setUpClass(cls): + cls.results = get_results("md/nve", "section_run") + cls.temp = convert_unit( + np.array([ + 300.000000000, + 275.075405378, + 235.091633019, + 202.752506973, + 192.266488819, + 201.629598676, + 218.299664775, + 230.324748557, + 232.691881533, + 226.146979313, + 213.165337396, + ]), + "K" + ) + cls.cons = convert_unit( + np.array([ + -34.323271136, + -34.323245645, + -34.323206964, + -34.323183380, + -34.323187747, + -34.323208962, + -34.323227533, + -34.323233583, + -34.323230715, + -34.323227013, + -34.323224123, + ]), + "hartree" + ) + cls.pot = convert_unit( + np.array([ + -34.330396471, + -34.329778993, + -34.328790653, + -34.327998978, + -34.327754290, + -34.327997890, + -34.328412394, + -34.328704052, + -34.328757407, + -34.328598255, + -34.328287038, + ]), + "hartree" + ) + cls.kin = convert_unit( + np.array([ + 0.007125335, + 0.006533348, + 0.005583688, + 0.004815598, + 0.004566544, + 0.004788928, + 0.005184860, + 0.005470470, + 0.005526692, + 0.005371243, + 0.005062914, + ]), + "hartree" + ) + + def test_number_of_atoms(self): + result = self.results["number_of_atoms"] + expected_result = np.array(50*[2]) + self.assertTrue(np.array_equal(result, expected_result)) + + def test_ensemble_type(self): + result = self.results["ensemble_type"] + self.assertEqual(result, "NVE") + + def test_sampling_method(self): + result = self.results["sampling_method"] + self.assertEqual(result, "molecular_dynamics") + + def test_number_of_frames_in_sequence(self): + result = self.results["number_of_frames_in_sequence"] + self.assertEqual(result, 50) + + def test_atom_positions(self): + result = self.results["atom_positions"] + expected_start = convert_unit( + np.array([ + [0.371489, 0.000511, 0.000554], + [-0.371489, -0.000511, -0.000554], + ]), + "angstrom" + ) + expected_end = convert_unit( + np.array([ + [0.391636, 0.024314, 0.026348], + [-0.391636, -0.024314, -0.026348], + ]), + "angstrom" + ) + self.assertTrue(np.array_equal(result[0, :], expected_start)) + self.assertTrue(np.array_equal(result[-1, :], expected_end)) + + # def test_atom_velocities(self): + # result = self.results["atom_velocities"] + # expected_start = convert_unit( + # np.array([ + # [0.0000299284, 0.0000082360, -0.0000216368], + # [-0.0001665963, 0.0001143863, -0.0000622640], + # [-0.0005732926, -0.0003112611, -0.0007149779], + # [0.0013083605, -0.0009262219, 0.0006258560], + # [0.0012002313, -0.0003701042, 0.0002810523], + # [0.0002340810, -0.0003388418, 0.0011398583], + # ]), + # "bohr*(planckConstant/hartree)^-1" + # ) + # expected_end = convert_unit( + # np.array([ + # [0.0001600263, -0.0000383308, 0.0000153662], + # [-0.0001269381, -0.0000005151, -0.0000726214], + # [0.0000177093, -0.0003257814, -0.0000257852], + # [-0.0015067045, -0.0001700489, -0.0003651605], + # [0.0000307926, 0.0006886719, 0.0008431321], + # [0.0007424681, 0.0003614127, 0.0005749089], + # ]), + # "bohr*(planckConstant/hartree)^-1" + # ) + + # self.assertTrue(np.array_equal(result[0,:], expected_start)) + # self.assertTrue(np.array_equal(result[-1,:], expected_end)) + + # def test_frame_sequence_potential_energy(self): + # result = self.results["frame_sequence_potential_energy"] + # self.assertTrue(np.array_equal(result, self.pot)) + + # def test_frame_sequence_kinetic_energy(self): + # result = self.results["frame_sequence_kinetic_energy"] + # self.assertTrue(np.array_equal(result, self.kin)) + + # def test_frame_sequence_conserved_quantity(self): + # result = self.results["frame_sequence_conserved_quantity"] + # self.assertTrue(np.array_equal(result, self.cons)) + + # def test_frame_sequence_temperature(self): + # result = self.results["frame_sequence_temperature"] + # self.assertTrue(np.array_equal(result, self.temp)) + + # def test_frame_sequence_time(self): + # result = self.results["frame_sequence_time"] + # expected_result = convert_unit( + # np.array([ + # 0.000000, + # 0.500000, + # 1.000000, + # 1.500000, + # 2.000000, + # 2.500000, + # 3.000000, + # 3.500000, + # 4.000000, + # 4.500000, + # 5.000000, + # ]), + # "fs" + # ) + # self.assertTrue(np.array_equal(result, expected_result)) + + # def test_frame_sequence_potential_energy_stats(self): + # result = self.results["frame_sequence_potential_energy_stats"] + # expected_result = np.array([self.pot.mean(), self.pot.std()]) + # self.assertTrue(np.array_equal(result, expected_result)) + + # def test_frame_sequence_kinetic_energy_stats(self): + # result = self.results["frame_sequence_kinetic_energy_stats"] + # expected_result = np.array([self.kin.mean(), self.kin.std()]) + # self.assertTrue(np.array_equal(result, expected_result)) + + # def test_frame_sequence_conserved_quantity_stats(self): + # result = self.results["frame_sequence_conserved_quantity_stats"] + # expected_result = np.array([self.cons.mean(), self.cons.std()]) + # self.assertTrue(np.array_equal(result, expected_result)) + + # def test_frame_sequence_temperature_stats(self): + # result = self.results["frame_sequence_temperature_stats"] + # expected_result = np.array([self.temp.mean(), self.temp.std()]) + # self.assertTrue(np.array_equal(result, expected_result)) + + # #=============================================================================== # class TestErrors(unittest.TestCase): # """Test misc. error stuations which may occur during the parsing. @@ -606,9 +798,6 @@ class TestGeoOpt(unittest.TestCase): # self.assertEqual(result, "120") - - - # # =============================================================================== # class TestGeoOptTrajFormats(unittest.TestCase): @@ -744,206 +933,6 @@ class TestGeoOpt(unittest.TestCase): # i_conf += 1 -# #=============================================================================== -# class TestMD(unittest.TestCase): - - # @classmethod - # def setUpClass(cls): - # cls.results = get_results("md/nve", "section_run") - # cls.temp = convert_unit( - # np.array([ - # 300.000000000, - # 275.075405378, - # 235.091633019, - # 202.752506973, - # 192.266488819, - # 201.629598676, - # 218.299664775, - # 230.324748557, - # 232.691881533, - # 226.146979313, - # 213.165337396, - # ]), - # "K" - # ) - # cls.cons = convert_unit( - # np.array([ - # -34.323271136, - # -34.323245645, - # -34.323206964, - # -34.323183380, - # -34.323187747, - # -34.323208962, - # -34.323227533, - # -34.323233583, - # -34.323230715, - # -34.323227013, - # -34.323224123, - # ]), - # "hartree" - # ) - # cls.pot = convert_unit( - # np.array([ - # -34.330396471, - # -34.329778993, - # -34.328790653, - # -34.327998978, - # -34.327754290, - # -34.327997890, - # -34.328412394, - # -34.328704052, - # -34.328757407, - # -34.328598255, - # -34.328287038, - # ]), - # "hartree" - # ) - # cls.kin = convert_unit( - # np.array([ - # 0.007125335, - # 0.006533348, - # 0.005583688, - # 0.004815598, - # 0.004566544, - # 0.004788928, - # 0.005184860, - # 0.005470470, - # 0.005526692, - # 0.005371243, - # 0.005062914, - # ]), - # "hartree" - # ) - - # def test_number_of_atoms(self): - # result = self.results["number_of_atoms"] - # expected_result = np.array(11*[6]) - # self.assertTrue(np.array_equal(result, expected_result)) - - # def test_ensemble_type(self): - # result = self.results["ensemble_type"] - # self.assertEqual(result, "NVE") - - # def test_sampling_method(self): - # result = self.results["sampling_method"] - # self.assertEqual(result, "molecular_dynamics") - - # def test_number_of_frames_in_sequence(self): - # result = self.results["number_of_frames_in_sequence"] - # self.assertEqual(result, 11) - - # def test_atom_positions(self): - # result = self.results["atom_positions"] - # expected_start = convert_unit( - # np.array([ - # [2.2803980000, 9.1465390000, 5.0886960000], - # [1.2517030000, 2.4062610000, 7.7699080000], - # [1.7620190000, 9.8204290000, 5.5284540000], - # [3.0959870000, 9.1070880000, 5.5881860000], - # [0.5541290000, 2.9826340000, 8.0820240000], - # [1.7712570000, 2.9547790000, 7.1821810000], - # ]), - # "angstrom" - # ) - # expected_end = convert_unit( - # np.array([ - # [2.2916014875, 9.1431763260, 5.0868100688], - # [1.2366834078, 2.4077552776, 7.7630044423], - # [1.6909790671, 9.8235337924, 5.5042564094], - # [3.1130341664, 9.0372111810, 5.6100739746], - # [0.5652070478, 3.0441761067, 8.1734257299], - # [1.8669280879, 2.9877213524, 7.2364955946], - # ]), - # "angstrom" - # ) - # self.assertTrue(np.array_equal(result[0,:], expected_start)) - # self.assertTrue(np.array_equal(result[-1,:], expected_end)) - - # def test_atom_velocities(self): - # result = self.results["atom_velocities"] - # expected_start = convert_unit( - # np.array([ - # [0.0000299284, 0.0000082360, -0.0000216368], - # [-0.0001665963, 0.0001143863, -0.0000622640], - # [-0.0005732926, -0.0003112611, -0.0007149779], - # [0.0013083605, -0.0009262219, 0.0006258560], - # [0.0012002313, -0.0003701042, 0.0002810523], - # [0.0002340810, -0.0003388418, 0.0011398583], - # ]), - # "bohr*(planckConstant/hartree)^-1" - # ) - # expected_end = convert_unit( - # np.array([ - # [0.0001600263, -0.0000383308, 0.0000153662], - # [-0.0001269381, -0.0000005151, -0.0000726214], - # [0.0000177093, -0.0003257814, -0.0000257852], - # [-0.0015067045, -0.0001700489, -0.0003651605], - # [0.0000307926, 0.0006886719, 0.0008431321], - # [0.0007424681, 0.0003614127, 0.0005749089], - # ]), - # "bohr*(planckConstant/hartree)^-1" - # ) - - # self.assertTrue(np.array_equal(result[0,:], expected_start)) - # self.assertTrue(np.array_equal(result[-1,:], expected_end)) - - # def test_frame_sequence_potential_energy(self): - # result = self.results["frame_sequence_potential_energy"] - # self.assertTrue(np.array_equal(result, self.pot)) - - # def test_frame_sequence_kinetic_energy(self): - # result = self.results["frame_sequence_kinetic_energy"] - # self.assertTrue(np.array_equal(result, self.kin)) - - # def test_frame_sequence_conserved_quantity(self): - # result = self.results["frame_sequence_conserved_quantity"] - # self.assertTrue(np.array_equal(result, self.cons)) - - # def test_frame_sequence_temperature(self): - # result = self.results["frame_sequence_temperature"] - # self.assertTrue(np.array_equal(result, self.temp)) - - # def test_frame_sequence_time(self): - # result = self.results["frame_sequence_time"] - # expected_result = convert_unit( - # np.array([ - # 0.000000, - # 0.500000, - # 1.000000, - # 1.500000, - # 2.000000, - # 2.500000, - # 3.000000, - # 3.500000, - # 4.000000, - # 4.500000, - # 5.000000, - # ]), - # "fs" - # ) - # self.assertTrue(np.array_equal(result, expected_result)) - - # def test_frame_sequence_potential_energy_stats(self): - # result = self.results["frame_sequence_potential_energy_stats"] - # expected_result = np.array([self.pot.mean(), self.pot.std()]) - # self.assertTrue(np.array_equal(result, expected_result)) - - # def test_frame_sequence_kinetic_energy_stats(self): - # result = self.results["frame_sequence_kinetic_energy_stats"] - # expected_result = np.array([self.kin.mean(), self.kin.std()]) - # self.assertTrue(np.array_equal(result, expected_result)) - - # def test_frame_sequence_conserved_quantity_stats(self): - # result = self.results["frame_sequence_conserved_quantity_stats"] - # expected_result = np.array([self.cons.mean(), self.cons.std()]) - # self.assertTrue(np.array_equal(result, expected_result)) - - # def test_frame_sequence_temperature_stats(self): - # result = self.results["frame_sequence_temperature_stats"] - # expected_result = np.array([self.temp.mean(), self.temp.std()]) - # self.assertTrue(np.array_equal(result, expected_result)) - - # #=============================================================================== # class TestMDEnsembles(unittest.TestCase): @@ -1045,8 +1034,9 @@ class TestGeoOpt(unittest.TestCase): #=============================================================================== if __name__ == '__main__': suites = [] - suites.append(unittest.TestLoader().loadTestsFromTestCase(TestSinglePoint)) - suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeoOpt)) - suites.append(unittest.TestLoader().loadTestsFromTestCase(TestInputParser)) + # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestSinglePoint)) + # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeoOpt)) + # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestInputParser)) + suites.append(unittest.TestLoader().loadTestsFromTestCase(TestMD)) alltests = unittest.TestSuite(suites) unittest.TextTestRunner(verbosity=0).run(alltests)