diff --git a/parser/parser-cpmd/cpmdparser/versions/cpmd41/commonparser.py b/parser/parser-cpmd/cpmdparser/versions/cpmd41/commonparser.py
index 21e040962fa5c25ef37dfcc462b9c6acde989704..b1670dce615cbbff1871467c08a101d604ef4aa8 100644
--- a/parser/parser-cpmd/cpmdparser/versions/cpmd41/commonparser.py
+++ b/parser/parser-cpmd/cpmdparser/versions/cpmd41/commonparser.py
@@ -27,6 +27,7 @@ class CPMDCommonParser(CommonParser):
self.cache_service.add("simulation_cell", single=False, update=False)
self.cache_service.add("n_steps")
self.cache_service.add("ensemble_type")
+ self.cache_service.add("time_step_ions")
#===========================================================================
# Common SimpleMatchers
@@ -75,8 +76,8 @@ class CPMDCommonParser(CommonParser):
SM( " NUMBER OF DISTINCT RESTART FILES:\s+{}".format(self.regexs.int)),
SM( " TEMPERATURE IS CALCULATED ASSUMING EXTENDED BULK BEHAVIOR"),
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( " TIME STEP FOR ELECTRONS:\s+(?P<x_cpmd_time_step_electrons__hbar_hartree_1>{})".format(self.regexs.float)),
+ SM( " TIME STEP FOR IONS:\s+(?P<x_cpmd_time_step_ions__hbar_hartree_1>{})".format(self.regexs.float)),
SM( " TRAJECTORIES ARE SAVED ON FILE"),
SM( " TRAJEC\.xyz IS SAVED ON FILE"),
@@ -281,8 +282,13 @@ class CPMDCommonParser(CommonParser):
# 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"
+ if temp_control is not None:
+ if temp_control.strip() == "THE TEMPERATURE IS NOT CONTROLLED":
+ self.cache_service["ensemble_type"] = "NVE"
+
+ # Ions time step
+ time_step_ions = section.get_latest_value("x_cpmd_time_step_ions")
+ self.cache_service["time_step_ions"] = time_step_ions
#===========================================================================
# adHoc functions
diff --git a/parser/parser-cpmd/cpmdparser/versions/cpmd41/mdparser.py b/parser/parser-cpmd/cpmdparser/versions/cpmd41/mdparser.py
index 956e32b7c2410ea97838e5822968bfb7f0e37a5e..b11d1d5c4bebb647f3b10447d8f875781e8f7872 100644
--- a/parser/parser-cpmd/cpmdparser/versions/cpmd41/mdparser.py
+++ b/parser/parser-cpmd/cpmdparser/versions/cpmd41/mdparser.py
@@ -30,6 +30,7 @@ class CPMDMDParser(MainHierarchicalParser):
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")
+ self.energies_filepath = self.file_service.get_absolute_path_to_file("ENERGIES")
#=======================================================================
# Cache levels
@@ -60,8 +61,24 @@ class CPMDMDParser(MainHierarchicalParser):
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(),
+ SM( " NFI EKINC TEMPP EKS ECLASSIC EHAM DIS TCPU"),
+ SM( re.escape(" * AVERAGED QUANTITIES *"),
+ sections=["x_cpmd_section_md_averaged_quantities"],
+ subMatchers=[
+ SM( re.escape(" MEAN VALUE +/- RMS DEVIATION")),
+ SM( re.escape(" <x> [<x^2>-<x>^2]**(1/2)")),
+ SM( " ELECTRON KINETIC ENERGY\s+(?P<x_cpmd_electron_kinetic_energy_mean>{0})\s+(?P<x_cpmd_electron_kinetic_energy_std>{0})".format(self.regexs.float)),
+ SM( " IONIC TEMPERATURE\s+(?P<x_cpmd_ionic_temperature_mean>{0})\s+(?P<x_cpmd_ionic_temperature_std>{0})".format(self.regexs.float)),
+ SM( " DENSITY FUNCTIONAL ENERGY\s+(?P<x_cpmd_density_functional_energy_mean>{0})\s+(?P<x_cpmd_density_functional_energy_std>{0})".format(self.regexs.float)),
+ SM( " CLASSICAL ENERGY\s+(?P<x_cpmd_classical_energy_mean>{0})\s+(?P<x_cpmd_classical_energy_std>{0})".format(self.regexs.float)),
+ SM( " CONSERVED ENERGY\s+(?P<x_cpmd_conserved_energy_mean>{0})\s+(?P<x_cpmd_conserved_energy_std>{0})".format(self.regexs.float)),
+ SM( " NOSE ENERGY ELECTRONS\s+(?P<x_cpmd_nose_energy_electrons_mean>{0})\s+(?P<x_cpmd_nose_energy_electrons_std>{0})".format(self.regexs.float)),
+ SM( " NOSE ENERGY IONS\s+(?P<x_cpmd_nose_energy_ions_mean>{0})\s+(?P<x_cpmd_nose_energy_ions_std>{0}) 0.000000 0.00000 ".format(self.regexs.float)),
+ SM( " CONSTRAINTS ENERGY\s+(?P<x_cpmd_constraints_energy_mean>{0})\s+(?P<x_cpmd_constraints_energy_std>{0})".format(self.regexs.float)),
+ SM( " RESTRAINTS ENERGY\s+(?P<x_cpmd_restraints_energy_mean>{0})\s+(?P<x_cpmd_restraints_energy_std>{0})".format(self.regexs.float)),
+ SM( " ION DISPLACEMENT\s+(?P<x_cpmd_ion_displacement_mean>{0})\s+(?P<x_cpmd_ion_displacement_std>{0})".format(self.regexs.float)),
+ SM( " CPU TIME\s+(?P<x_cpmd_cpu_time_mean>{0})".format(self.regexs.float)),
+ ]
),
self.cm.footer(),
]
@@ -69,91 +86,142 @@ class CPMDMDParser(MainHierarchicalParser):
#=======================================================================
# 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")
+ def onClose_x_cpmd_section_md_averaged_quantities(self, backend, gIndex, section):
+ cons_mean = section.get_latest_value("x_cpmd_conserved_energy_mean")
+ cons_std = section.get_latest_value("x_cpmd_conserved_energy_std")
+ temp_mean = section.get_latest_value("x_cpmd_ionic_temperature_mean")
+ temp_std = section.get_latest_value("x_cpmd_ionic_temperature_std")
+ pot_mean = section.get_latest_value("x_cpmd_density_functional_energy_mean")
+ pot_std = section.get_latest_value("x_cpmd_density_functional_energy_std")
+
+ self.parse_md()
+ backend.addArrayValues("frame_sequence_temperature_stats", np.array([temp_mean, temp_std]), unit="K")
+ backend.addArrayValues("frame_sequence_conserved_quantity_stats", np.array([cons_mean, cons_std]), unit="hartree")
+ backend.addArrayValues("frame_sequence_potential_energy_stats", np.array([pot_mean, pot_std]), unit="hartree")
#=======================================================================
# adHoc
- def ad_hoc_parse_md(self):
+ def 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
+ # Decide from which file trajectory is read
+ traj_file = None
+ traj_step = 1
+ trajec_file_iterator = None
+ if self.dcd_filepath is not None:
+ traj_file = self.dcd_filepath
+ elif self.xyz_filepath is not None:
+ traj_file = self.xyz_filepath
+
+ # Initialize the TRAJEC file iterator
+ if traj_file is not None:
+ try:
+ trajec_file_iterator = nomadcore.configurationreading.iread(traj_file)
+ except ValueError:
+ pass
+
+ # Initialize the TRAJECTORY file iterator
+ trajectory_file_iterator = None
+ if self.trajectory_filepath is not None:
+ n_atoms = self.cache_service["number_of_atoms"]
+ trajectory_file_iterator = nomadcore.csvparsing.iread(self.trajectory_filepath, columns=range(7), n_conf=n_atoms)
+
+ # Initialize the ENERGIES file iterator
+ energies_iterator = nomadcore.csvparsing.iread(self.energies_filepath, columns=range(8))
+
+ # Start reading the frames
+ i_frame = 0
+ n_frames = self.cache_service["n_steps"]
+ time_step = self.cache_service["time_step_ions"]
+ self.backend.addArrayValues("frame_sequence_time", np.array([(x+1)*time_step for x in range(n_frames)]))
+ self.backend.addValue("number_of_frames_in_sequence", n_frames)
+
+ temperatures = []
+ potential_energies = []
+ kinetic_energies = []
+ conserved_quantities = []
+
+ for i_frame in range(n_frames):
+
+ # Open sections
+ scc_id = self.backend.openSection("section_single_configuration_calculation")
+ sys_id = self.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")
+
+ # TRAJEC file
+ if trajec_file_iterator is not None:
if i_frame % traj_step == 0:
try:
- pos = next(traj_iterator)
+ pos = next(trajec_file_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.")
+ LOGGER.error("Could not get the next geometries from a TRAJEC file.")
else:
- parser.backend.addArrayValues("atom_positions", pos, unit=traj_unit)
+ self.backend.addArrayValues("atom_positions", pos, unit="angstrom")
- parser.backend.closeSection("section_single_configuration_calculation", scc_id)
- parser.backend.closeSection("section_system", sys_id)
-
- return wrapper
+ # TRAJECTORY file
+ if trajectory_file_iterator is not None:
+ try:
+ values = next(trajectory_file_iterator)
+ except StopIteration:
+ LOGGER.error("Could not get the next configuration from a TRAJECTORY file.")
+ else:
+ velocities = values[:, 4:]
+ self.backend.addArrayValues("atom_velocities", velocities, unit="bohr/(hbar/hartree)")
+
+ if trajec_file_iterator is None:
+ pos = values[:, 1:4]
+ self.backend.addArrayValues("atom_positions", pos, unit="bohr")
+
+ # Energies file
+ if energies_iterator is not None:
+ try:
+ values = next(energies_iterator)
+ except StopIteration:
+ LOGGER.error("Could not get the next configuration from an ENERGIES file.")
+ else:
+ potential_energy = values[3]
+ conserved_quantity = values[5]
+ ion_total_energy = values[4]
+ kinetic_energy = ion_total_energy - potential_energy
+ temperature = values[2]
+ # electronic_kinetic_energy = values[1]
+ # msd = values[6]
+ # i_step = values[0]
+ tcpu = values[7]
+ conserved_quantities.append(conserved_quantity)
+ potential_energies.append(potential_energy)
+ kinetic_energies.append(kinetic_energy)
+ temperatures.append(temperature)
+ self.backend.addRealValue("energy_total", potential_energy, unit="hartree")
+ self.backend.addValue("time_calculation", tcpu)
+
+ # Close sections
+ self.backend.closeSection("section_single_configuration_calculation", scc_id)
+ self.backend.closeSection("section_system", sys_id)
+
+ # Push the summaries
+ potential_energies = np.array(potential_energies)
+ self.backend.addArrayValues("frame_sequence_potential_energy", potential_energies, unit="hartree")
+ kinetic_energies = np.array(kinetic_energies)
+ self.backend.addArrayValues("frame_sequence_kinetic_energy", kinetic_energies, unit="hartree")
+ conserved_quantities = np.array(conserved_quantities)
+ self.backend.addArrayValues("frame_sequence_conserved_quantity", conserved_quantities, unit="hartree")
+ temperatures = np.array(temperatures)
+ self.backend.addArrayValues("frame_sequence_temperature", temperatures, unit="K")
+
+ # Push the statistics. CPMD prints some statistics at the end, but the
+ # mean and std of kinetic energy are missing
+ kin_mean = kinetic_energies.mean()
+ kin_temp = (kinetic_energies - kin_mean)
+ kin_std = np.sqrt(np.dot(kin_temp, kin_temp)/kinetic_energies.size)
+ kin_temp = None
+ self.backend.addArrayValues("frame_sequence_kinetic_energy_stats", np.array([kin_mean, kin_std]), unit="hartree")
diff --git a/test/unittests/cpmd_4.1/md/dcd/ENERGIES b/test/unittests/cpmd_4.1/md/dcd/ENERGIES
index 3cd94f657c6274216f449d6533ca06f6441ee5e1..81ab5944a26e216aa8e81b473b35698c649d5a9c 100644
--- a/test/unittests/cpmd_4.1/md/dcd/ENERGIES
+++ b/test/unittests/cpmd_4.1/md/dcd/ENERGIES
@@ -1,50 +1,5 @@
- 1 0.00472945 110.096 -1.1023492072 -1.1018262261 -1.0970967730 0.288545E-05 0.24
+ 1 0.00472945 110.096 -1.1023492072 -1.1018262261 -1.0970967730 0.288545E-05 0.29
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 0.23
+ 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 0.24
- 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 0.23
- 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 0.22
- 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 0.22
- 17 0.01776074 44.244 -1.1153899632 -1.1151797929 -1.0974190575 0.112264E-02 0.23
- 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 0.22
- 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 0.23
- 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 0.24
- 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 0.23
- 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 0.23
- 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 0.23
- 40 0.01744917 44.419 -1.1150750202 -1.1148640199 -1.0974148488 0.473558E-02 0.22
- 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 0.22
- 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 0.23
- 47 0.01826876 44.768 -1.1159079382 -1.1156952780 -1.0974265218 0.575782E-02 0.22
- 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 0.22
- 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/dcd/GEOMETRY b/test/unittests/cpmd_4.1/md/dcd/GEOMETRY
index 99afcdea42b2a843f164962a4b29f8f63c16e0db..5209a7da40841355f0f4a8ebe66f3f6b212e2da1 100644
--- a/test/unittests/cpmd_4.1/md/dcd/GEOMETRY
+++ b/test/unittests/cpmd_4.1/md/dcd/GEOMETRY
@@ -1,2 +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
+ 0.715304751615 0.004785368892 0.005185649980 0.000946442689 0.000235633854 0.000255343887
+ -0.715304751615 -0.004785368892 -0.005185649980 -0.000946442689 -0.000235633854 -0.000255343887
diff --git a/test/unittests/cpmd_4.1/md/dcd/GEOMETRY.xyz b/test/unittests/cpmd_4.1/md/dcd/GEOMETRY.xyz
index 15b6e3715df41db74f68e973a4f400d438925ea8..644d2c0c17085461cbc66efb46bfc7ea7b45720e 100644
--- a/test/unittests/cpmd_4.1/md/dcd/GEOMETRY.xyz
+++ b/test/unittests/cpmd_4.1/md/dcd/GEOMETRY.xyz
@@ -1,4 +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
+ H 0.378522973374 0.002532308163 0.002744127793 0.000500835903 0.000124692066 0.000135122166
+ H -0.378522973374 -0.002532308163 -0.002744127793 -0.000500835903 -0.000124692066 -0.000135122166
diff --git a/test/unittests/cpmd_4.1/md/dcd/RESTART.1 b/test/unittests/cpmd_4.1/md/dcd/RESTART.1
index 1ca9d0b7f223eda2adabc2c8dcab08e74d2ce166..804eeb9491a7ba3e4de4c1f038fe0a14afe29e1a 100644
Binary files a/test/unittests/cpmd_4.1/md/dcd/RESTART.1 and b/test/unittests/cpmd_4.1/md/dcd/RESTART.1 differ
diff --git a/test/unittests/cpmd_4.1/md/dcd/TRAJEC.dcd b/test/unittests/cpmd_4.1/md/dcd/TRAJEC.dcd
index e8fc4f6b37c81c219953bbe8f341153537fe3eca..5cfb50b19ec9b4a522b2b181ed653880654ae796 100644
Binary files a/test/unittests/cpmd_4.1/md/dcd/TRAJEC.dcd and b/test/unittests/cpmd_4.1/md/dcd/TRAJEC.dcd differ
diff --git a/test/unittests/cpmd_4.1/md/dcd/TRAJECTORY b/test/unittests/cpmd_4.1/md/dcd/TRAJECTORY
index 938315e8aa26e0a107af689e5ee1e95ca0febae0..a2177c5422573451e5a04350da1e8d13bc79a8ed 100644
--- a/test/unittests/cpmd_4.1/md/dcd/TRAJECTORY
+++ b/test/unittests/cpmd_4.1/md/dcd/TRAJECTORY
@@ -8,93 +8,3 @@
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
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
- 6 -0.71893399424602 -0.00572444997561 -0.00620328225215 -0.00082839676152 -0.00023386099777 -0.00025342273759
- 7 0.72193192570691 0.00665625687434 0.00721303188086 0.00065043437225 0.00023204071799 0.00025145019840
- 7 -0.72193192570691 -0.00665625687434 -0.00721303188086 -0.00065043437225 -0.00023204071799 -0.00025145019840
- 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
- 9 0.72554542133177 0.00849834188842 0.00920920156151 0.00026604758553 0.00022865706989 0.00024778352359
- 9 -0.72554542133177 -0.00849834188842 -0.00920920156151 -0.00026604758553 -0.00022865706989 -0.00024778352359
- 10 0.72626584990829 0.00941003227866 0.01019715202805 0.00011553435138 0.00022739762125 0.00024641872984
- 10 -0.72626584990828 -0.00941003227866 -0.01019715202805 -0.00011553435138 -0.00022739762125 -0.00024641872984
- 11 0.72646969614282 0.01031752285845 0.01118055140022 0.00000919157561 0.00022656626230 0.00024551783523
- 11 -0.72646969614281 -0.01031752285845 -0.01118055140022 -0.00000919157561 -0.00022656626230 -0.00024551783523
- 12 0.72633938251320 0.01122256237707 0.01216129470990 -0.00005391350069 0.00022617397185 0.00024509273727
- 12 -0.72633938251319 -0.01122256237707 -0.01216129470990 0.00005391350069 -0.00022617397185 -0.00024509273727
- 13 0.72603838813733 0.01212691463322 0.01314129329840 -0.00008020751653 0.00022621309441 0.00024513514017
- 13 -0.72603838813732 -0.01212691463322 -0.01314129329840 0.00008020751653 -0.00022621309441 -0.00024513514017
- 14 0.72569772238094 0.01303226713237 0.01412237583128 -0.00007837151973 0.00022661957795 0.00024557563428
- 14 -0.72569772238093 -0.01303226713237 -0.01412237583128 0.00007837151973 -0.00022661957795 -0.00024557563428
- 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
- 16 0.72523999871705 0.01485059680662 0.01609280348805 -0.00002416178131 0.00022815395964 0.00024723838775
- 16 -0.72523999871704 -0.01485059680662 -0.01609280348805 0.00002416178131 -0.00022815395964 -0.00024723838775
- 17 0.72521812172908 0.01576510293390 0.01708380547460 0.00001507794579 0.00022913474609 0.00024830123034
- 17 -0.72521812172908 -0.01576510293391 -0.01708380547460 -0.00001507794579 -0.00022913474609 -0.00024830123034
- 18 0.72536062228341 0.01668367477532 0.01807921333078 0.00005625041435 0.00023014808425 0.00024939935061
- 18 -0.72536062228340 -0.01668367477532 -0.01807921333078 -0.00005625041435 -0.00023014808425 -0.00024939935061
- 19 0.72566812504388 0.01760628760793 0.01907900027949 0.00009650087857 0.00023114641406 0.00025048121053
- 19 -0.72566812504387 -0.01760628760793 -0.01907900027949 -0.00009650087857 -0.00023114641406 -0.00025048121053
- 20 0.72613262931195 0.01853284608778 0.02008306301505 0.00013403687154 0.00023209856863 0.00025151303647
- 20 -0.72613262931194 -0.01853284608778 -0.02008306301505 -0.00013403687154 -0.00023209856863 -0.00025151303647
- 21 0.72674042001620 0.01946307615693 0.02109110457125 0.00016766415629 0.00023295798887 0.00025244437542
- 21 -0.72674042001620 -0.01946307615693 -0.02109110457125 -0.00016766415629 -0.00023295798887 -0.00025244437542
- 22 0.72747394256230 0.02039650999872 0.02210261801843 0.00019672664260 0.00023370463452 0.00025325351120
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- 23 -0.72831423315702 -0.02133271323312 -0.02311713266083 -0.00022098344374 -0.00023433759982 -0.00025393946265
- 24 0.72924181011222 0.02227121079730 0.02413413371961 0.00024032818130 0.00023483603069 0.00025447963179
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- 25 0.73023685860739 0.02321140147860 0.02515296971514 0.00025481624125 0.00023519298119 0.00025486649200
- 25 -0.73023685860739 -0.02321140147860 -0.02515296971514 -0.00025481624125 -0.00023519298119 -0.00025486649200
- 26 0.73128034004219 0.02415275464679 0.02617306565557 0.00026467349225 0.00023542168715 0.00025511438699
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- 27 0.73235424654535 0.02509477497584 0.02719388481103 0.00027010758805 0.00023551447637 0.00025521500303
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- 28 0.73344120074658 0.02603687045779 0.02821478567984 0.00027134564227 0.00023546694185 0.00025516356438
- 28 -0.73344120074658 -0.02603687045779 -0.02821478567984 -0.00027134564227 -0.00023546694185 -0.00025516356438
- 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
- 30 0.73559077265617 0.02791923312252 0.03025460713037 0.00026241162068 0.00023499769277 0.00025465523294
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- 31 0.73662430464896 0.02885849205281 0.03127243518962 0.00025272074446 0.00023456774370 0.00025418941566
- 31 -0.73662430464896 -0.02885849205281 -0.03127243518962 -0.00025272074446 -0.00023456774370 -0.00025418941566
- 32 0.73761253861181 0.02979577507214 0.03228812245563 0.00023992413820 0.00023402010459 0.00025359607392
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- 33 0.73854369775457 0.03073065288949 0.03330120378100 0.00022427440798 0.00023335689709 0.00025287750774
- 33 -0.73854369775457 -0.03073065288950 -0.03330120378100 -0.00022427440798 -0.00023335689709 -0.00025287750774
- 34 0.73940673387562 0.03166263024882 0.03431114251756 0.00020599682177 0.00023257175449 0.00025202681362
- 34 -0.73940673387561 -0.03166263024882 -0.03431114251756 -0.00020599682177 -0.00023257175449 -0.00025202681362
- 35 0.74019167232872 0.03259122692542 0.03531741828998 0.00018541181754 0.00023167860378 0.00025105908813
- 35 -0.74019167232872 -0.03259122692542 -0.03531741828998 -0.00018541181754 -0.00023167860378 -0.00025105908813
- 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
- 37 0.74149444230477 0.03443672134444 0.03731729409361 0.00013864647024 0.00022959911555 0.00024880596230
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- 38 0.74199920017784 0.03535285200351 0.03831006292093 0.00011333074516 0.00022843904823 0.00024754902429
- 38 -0.74199920017784 -0.03535285200351 -0.03831006292093 -0.00011333074516 -0.00022843904823 -0.00024754902429
- 39 0.74240108826605 0.03626423373030 0.03929768628789 0.00008747527307 0.00022723141891 0.00024624056979
- 39 -0.74240108826605 -0.03626423373031 -0.03929768628789 -0.00008747527307 -0.00022723141891 -0.00024624056979
- 40 0.74269900236237 0.03717070335480 0.04027998747923 0.00006153996769 0.00022599290438 0.00024489865284
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- 42 0.74298581133387 0.03896865178777 0.04222834743813 0.00001048866569 0.00022348267808 0.00024217888239
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- 43 -0.74297731733313 -0.03986003838995 -0.04319430656967 0.00001474968690 -0.00022219565239 -0.00024078445181
- 44 0.74286781383868 0.04074621700688 0.04415462305260 -0.00004009642226 0.00022088100968 0.00023936007438
- 44 -0.74286781383868 -0.04074621700688 -0.04415462305261 0.00004009642226 -0.00022088100968 -0.00023936007438
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- 45 -0.74265654595502 -0.04162708646739 -0.04510918716471 0.00006564676576 -0.00021952106504 -0.00023788664062
- 46 0.74234263971264 0.04250238552716 0.04605771617754 -0.00009134238039 0.00021810231001 0.00023634953748
- 46 -0.74234263971264 -0.04250238552717 -0.04605771617754 0.00009134238039 -0.00021810231001 -0.00023634953748
- 47 0.74192580691191 0.04337190494748 0.04699998346457 -0.00011688598986 0.00021667055455 0.00023479831214
- 47 -0.74192580691191 -0.04337190494748 -0.04699998346457 0.00011688598986 -0.00021667055455 -0.00023479831214
- 48 0.74140755179378 0.04423574996358 0.04793610267467 -0.00014176306461 0.00021525878766 0.00023326873051
- 48 -0.74140755179378 -0.04423574996359 -0.04793610267468 0.00014176306461 -0.00021525878766 -0.00023326873051
- 49 0.74079170239500 0.04509397524877 0.04886613330868 -0.00016538618998 0.00021385628867 0.00023174930644
- 49 -0.74079170239500 -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
index 3b5f6e58cc8169e08d9a7dda65f223948666cc8a..ed99c8b3da73bb2266f9bd3d3c174b62d18c2a6f 100755
--- a/test/unittests/cpmd_4.1/md/dcd/input.inp
+++ b/test/unittests/cpmd_4.1/md/dcd/input.inp
@@ -12,7 +12,7 @@ simple molecular dynamics deltat=4au
50.0D0
MAXSTEP
- 50
+ 5
TIMESTEP
4.0
&END
diff --git a/test/unittests/cpmd_4.1/md/dcd/output.out b/test/unittests/cpmd_4.1/md/dcd/output.out
index b0c9787d3951165b0d4048e0c16dc0311f557c4d..a7ee8dcc41b8778c2d4027dd03929df32549428b 100644
--- a/test/unittests/cpmd_4.1/md/dcd/output.out
+++ b/test/unittests/cpmd_4.1/md/dcd/output.out
@@ -1,5 +1,5 @@
cp_groups: we are using a 1 x 1 grid (groups x nprocs).
- PROGRAM CPMD STARTED AT: 2016-07-26 14:19:39.304
+ PROGRAM CPMD STARTED AT: 2016-07-27 18:28:14.778
SETCNST| USING: CODATA 2006 UNITS
@@ -32,7 +32,7 @@
/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 PROCESS ID IS: 23207
THE JOB WAS SUBMITTED BY: lauri
@@ -50,7 +50,7 @@
ITERATIVE ORTHOGONALIZATION
MAXIT: 30
EPS: 1.00E-06
- MAXIMUM NUMBER OF STEPS: 50 STEPS
+ MAXIMUM NUMBER OF STEPS: 5 STEPS
MAXIMUM NUMBER OF ITERATIONS FOR SC: 10000 STEPS
PRINT INTERMEDIATE RESULTS EVERY 10001 STEPS
STORE INTERMEDIATE RESULTS EVERY 10001 STEPS
@@ -189,7 +189,7 @@
== END OF FORCES INITIALIZATION ==
================================================================
- TIME FOR INITIALIZATION: 1.06 SECONDS
+ TIME FOR INITIALIZATION: 1.12 SECONDS
****************************************************************
* ATOMIC COORDINATES *
@@ -213,57 +213,12 @@
(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
+ 1 0.00473 110.1 -1.10235 -1.10183 -1.09710 0.289E-05 0.29
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
+ 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 0.24
- 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
@@ -272,17 +227,17 @@
****************************************************************
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
+ ELECTRON KINETIC ENERGY 0.018451 0.800503E-02
+ IONIC TEMPERATURE 300.0613 113.733
+ DENSITY FUNCTIONAL ENERGY -1.117412 0.876222E-02
+ CLASSICAL ENERGY -1.115986 0.822265E-02
+ CONSERVED ENERGY -1.097536 0.234060E-03
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
+ ION DISPLACEMENT 0.940474E-04 0.917156E-04
+ CPU TIME 0.2500
****************************************************************
* *
@@ -293,8 +248,8 @@
****************************************************************
* ATOMIC COORDINATES *
****************************************************************
- 1 H 0.740084 0.045947 0.049790
- 2 H -0.740084 -0.045947 -0.049790
+ 1 H 0.715305 0.004785 0.005186
+ 2 H -0.715305 -0.004785 -0.005186
****************************************************************
@@ -302,20 +257,20 @@
ELECTRONIC GRADIENT:
- MAX. COMPONENT = 1.39929E-02 NORM = 2.08955E-03
+ MAX. COMPONENT = 7.46544E-03 NORM = 1.85389E-03
TOTAL INTEGRATED ELECTRONIC DENSITY
- IN G-SPACE = 1.9999999999
- IN R-SPACE = 1.9999999999
+ IN G-SPACE = 1.9999999998
+ IN R-SPACE = 1.9999999998
- (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.
+ (K+E1+L+N+X) TOTAL ENERGY = -1.12453355 A.U.
+ (K) KINETIC ENERGY = 1.11789875 A.U.
+ (E1=A-S+R) ELECTROSTATIC ENERGY = -0.47871616 A.U.
(S) ESELF = 0.66490380 A.U.
- (R) ESR = 0.14497305 A.U.
- (L) LOCAL PSEUDOPOTENTIAL ENERGY = -1.04064388 A.U.
+ (R) ESR = 0.16297859 A.U.
+ (L) LOCAL PSEUDOPOTENTIAL ENERGY = -1.11784096 A.U.
(N) N-L PSEUDOPOTENTIAL ENERGY = 0.00000000 A.U.
- (X) EXCHANGE-CORRELATION ENERGY = -0.63585977 A.U.
+ (X) EXCHANGE-CORRELATION ENERGY = -0.64587518 A.U.
****************************************************************
@@ -328,48 +283,47 @@
****************************************************************
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
+ cpmd 1 0.01 0.01 2.87 2.87
+ mdpt 1 0.00 0.00 2.37 2.37
+ mdmain 1 0.00 0.00 2.37 2.37
+ forcedr 6 0.00 0.00 1.51 1.51
+ forces 6 0.00 0.00 1.51 1.51
+ vofrho 7 0.00 0.00 1.30 1.30
+ forces_a 6 0.00 0.00 1.19 1.19
+ rscpot 6 0.00 0.00 1.19 1.19
+ VOFRHOB 7 0.03 0.03 0.86 0.86
+ initrun 1 0.00 0.00 0.85 0.85
+ rinitwf 1 0.00 0.00 0.85 0.85
+ ATOMWF 1 0.00 0.00 0.85 0.85
+ INVFFTN 22 0.76 0.76 0.76 0.76
+ xcener_new 7 0.03 0.03 0.49 0.49
+ mikeu 7 0.47 0.47 0.47 0.47
+ FWFFTN 15 0.46 0.46 0.46 0.46
+ VOFRHOA 7 0.01 0.01 0.43 0.43
+ vpsi 8 0.04 0.04 0.42 0.42
+ ATRHO 1 0.36 0.36 0.41 0.41
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
+ rhoofr 6 0.05 0.05 0.23 0.23
NUMPW 1 0.12 0.12 0.12 0.12
- RINFORCE 1 0.00 0.00 0.10 0.10
+ RINFORCE 1 0.00 0.00 0.11 0.11
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
+ potfor 6 0.06 0.06 0.06 0.06
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
+ ppener 7 0.04 0.04 0.04 0.04
+ EICALC 7 0.03 0.03 0.03 0.03
+ PUTPS 1 0.01 0.01 0.01 0.01
+ fftprp 1 0.00 0.00 0.00 0.00
+ ovlap 17 0.00 0.00 0.00 0.00
+ VELUPA 10 0.00 0.00 0.00 0.00
****************************************************************
- CPU TIME : 0 HOURS 0 MINUTES 12.98 SECONDS
- ELAPSED TIME : 0 HOURS 0 MINUTES 13.00 SECONDS
+ CPU TIME : 0 HOURS 0 MINUTES 2.87 SECONDS
+ ELAPSED TIME : 0 HOURS 0 MINUTES 2.87 SECONDS
*** CPMD| SIZE OF THE PROGRAM IS NOT AVAILABLE ***
- PROGRAM CPMD ENDED AT: 2016-07-26 14:19:52.304
+ PROGRAM CPMD ENDED AT: 2016-07-27 18:28:17.650
diff --git a/test/unittests/cpmd_4.1/md/nve/ENERGIES b/test/unittests/cpmd_4.1/md/nve/ENERGIES
index 3779f299b02fbce5ef6fbb2303f56c6cf2d640e7..2e1b5cffe89fecba53fe53e3f5050b70cdfd1703 100644
--- a/test/unittests/cpmd_4.1/md/nve/ENERGIES
+++ b/test/unittests/cpmd_4.1/md/nve/ENERGIES
@@ -1,50 +1,5 @@
- 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
+ 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 0.24
+ 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 0.24
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/unittests/cpmd_4.1/md/nve/GEOMETRY b/test/unittests/cpmd_4.1/md/nve/GEOMETRY
index 99afcdea42b2a843f164962a4b29f8f63c16e0db..5209a7da40841355f0f4a8ebe66f3f6b212e2da1 100644
--- a/test/unittests/cpmd_4.1/md/nve/GEOMETRY
+++ b/test/unittests/cpmd_4.1/md/nve/GEOMETRY
@@ -1,2 +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
+ 0.715304751615 0.004785368892 0.005185649980 0.000946442689 0.000235633854 0.000255343887
+ -0.715304751615 -0.004785368892 -0.005185649980 -0.000946442689 -0.000235633854 -0.000255343887
diff --git a/test/unittests/cpmd_4.1/md/nve/GEOMETRY.xyz b/test/unittests/cpmd_4.1/md/nve/GEOMETRY.xyz
index 15b6e3715df41db74f68e973a4f400d438925ea8..644d2c0c17085461cbc66efb46bfc7ea7b45720e 100644
--- a/test/unittests/cpmd_4.1/md/nve/GEOMETRY.xyz
+++ b/test/unittests/cpmd_4.1/md/nve/GEOMETRY.xyz
@@ -1,4 +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
+ H 0.378522973374 0.002532308163 0.002744127793 0.000500835903 0.000124692066 0.000135122166
+ H -0.378522973374 -0.002532308163 -0.002744127793 -0.000500835903 -0.000124692066 -0.000135122166
diff --git a/test/unittests/cpmd_4.1/md/nve/RESTART.1 b/test/unittests/cpmd_4.1/md/nve/RESTART.1
index 146dd1cb90e5bff9998ad2a2567dcf3167124809..7ce3c028478c60d90cc0e4a4374c823cbc0526dd 100644
Binary files a/test/unittests/cpmd_4.1/md/nve/RESTART.1 and b/test/unittests/cpmd_4.1/md/nve/RESTART.1 differ
diff --git a/test/unittests/cpmd_4.1/md/nve/TRAJEC.xyz b/test/unittests/cpmd_4.1/md/nve/TRAJEC.xyz
index a550acbe47e5c4d4cdbabaf65041ca6e70a0fa95..fee8c8bf77f773de37d0a9814c1e80b2ac365089 100644
--- a/test/unittests/cpmd_4.1/md/nve/TRAJEC.xyz
+++ b/test/unittests/cpmd_4.1/md/nve/TRAJEC.xyz
@@ -18,183 +18,3 @@
STEP: 5
H 0.378523 0.002532 0.002744
H -0.378523 -0.002532 -0.002744
- 2
- STEP: 6
- H 0.380443 0.003029 0.003283
- H -0.380443 -0.003029 -0.003283
- 2
- STEP: 7
- H 0.382030 0.003522 0.003817
- H -0.382030 -0.003522 -0.003817
- 2
- STEP: 8
- H 0.383197 0.004012 0.004347
- H -0.383197 -0.004012 -0.004347
- 2
- STEP: 9
- H 0.383942 0.004497 0.004873
- H -0.383942 -0.004497 -0.004873
- 2
- STEP: 10
- H 0.384323 0.004980 0.005396
- H -0.384323 -0.004980 -0.005396
- 2
- STEP: 11
- H 0.384431 0.005460 0.005916
- H -0.384431 -0.005460 -0.005916
- 2
- STEP: 12
- H 0.384362 0.005939 0.006435
- H -0.384362 -0.005939 -0.006435
- 2
- STEP: 13
- H 0.384203 0.006417 0.006954
- H -0.384203 -0.006417 -0.006954
- 2
- STEP: 14
- H 0.384023 0.006896 0.007473
- H -0.384023 -0.006896 -0.007473
- 2
- STEP: 15
- H 0.383871 0.007377 0.007994
- H -0.383871 -0.007377 -0.007994
- 2
- STEP: 16
- H 0.383780 0.007859 0.008516
- H -0.383780 -0.007859 -0.008516
- 2
- STEP: 17
- H 0.383769 0.008343 0.009040
- H -0.383769 -0.008343 -0.009040
- 2
- STEP: 18
- H 0.383844 0.008829 0.009567
- H -0.383844 -0.008829 -0.009567
- 2
- STEP: 19
- H 0.384007 0.009317 0.010096
- H -0.384007 -0.009317 -0.010096
- 2
- STEP: 20
- H 0.384253 0.009807 0.010627
- H -0.384253 -0.009807 -0.010627
- 2
- STEP: 21
- H 0.384574 0.010299 0.011161
- H -0.384574 -0.010299 -0.011161
- 2
- STEP: 22
- H 0.384963 0.010793 0.011696
- H -0.384963 -0.010793 -0.011696
- 2
- STEP: 23
- H 0.385407 0.011289 0.012233
- H -0.385407 -0.011289 -0.012233
- 2
- STEP: 24
- H 0.385898 0.011785 0.012771
- H -0.385898 -0.011785 -0.012771
- 2
- STEP: 25
- H 0.386425 0.012283 0.013310
- H -0.386425 -0.012283 -0.013310
- 2
- STEP: 26
- H 0.386977 0.012781 0.013850
- H -0.386977 -0.012781 -0.013850
- 2
- STEP: 27
- H 0.387545 0.013280 0.014390
- H -0.387545 -0.013280 -0.014390
- 2
- STEP: 28
- H 0.388120 0.013778 0.014931
- H -0.388120 -0.013778 -0.014931
- 2
- STEP: 29
- H 0.388694 0.014276 0.015471
- H -0.388694 -0.014276 -0.015471
- 2
- STEP: 30
- H 0.389258 0.014774 0.016010
- H -0.389258 -0.014774 -0.016010
- 2
- STEP: 31
- H 0.389805 0.015271 0.016549
- H -0.389805 -0.015271 -0.016549
- 2
- STEP: 32
- H 0.390328 0.015767 0.017086
- H -0.390328 -0.015767 -0.017086
- 2
- STEP: 33
- H 0.390820 0.016262 0.017622
- H -0.390820 -0.016262 -0.017622
- 2
- STEP: 34
- H 0.391277 0.016755 0.018157
- H -0.391277 -0.016755 -0.018157
- 2
- STEP: 35
- H 0.391693 0.017247 0.018689
- H -0.391693 -0.017247 -0.018689
- 2
- STEP: 36
- H 0.392062 0.017736 0.019220
- H -0.392062 -0.017736 -0.019220
- 2
- STEP: 37
- H 0.392382 0.018223 0.019747
- H -0.392382 -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/nve/TRAJECTORY b/test/unittests/cpmd_4.1/md/nve/TRAJECTORY
index 938315e8aa26e0a107af689e5ee1e95ca0febae0..a2177c5422573451e5a04350da1e8d13bc79a8ed 100644
--- a/test/unittests/cpmd_4.1/md/nve/TRAJECTORY
+++ b/test/unittests/cpmd_4.1/md/nve/TRAJECTORY
@@ -8,93 +8,3 @@
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
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
- 6 -0.71893399424602 -0.00572444997561 -0.00620328225215 -0.00082839676152 -0.00023386099777 -0.00025342273759
- 7 0.72193192570691 0.00665625687434 0.00721303188086 0.00065043437225 0.00023204071799 0.00025145019840
- 7 -0.72193192570691 -0.00665625687434 -0.00721303188086 -0.00065043437225 -0.00023204071799 -0.00025145019840
- 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
- 9 0.72554542133177 0.00849834188842 0.00920920156151 0.00026604758553 0.00022865706989 0.00024778352359
- 9 -0.72554542133177 -0.00849834188842 -0.00920920156151 -0.00026604758553 -0.00022865706989 -0.00024778352359
- 10 0.72626584990829 0.00941003227866 0.01019715202805 0.00011553435138 0.00022739762125 0.00024641872984
- 10 -0.72626584990828 -0.00941003227866 -0.01019715202805 -0.00011553435138 -0.00022739762125 -0.00024641872984
- 11 0.72646969614282 0.01031752285845 0.01118055140022 0.00000919157561 0.00022656626230 0.00024551783523
- 11 -0.72646969614281 -0.01031752285845 -0.01118055140022 -0.00000919157561 -0.00022656626230 -0.00024551783523
- 12 0.72633938251320 0.01122256237707 0.01216129470990 -0.00005391350069 0.00022617397185 0.00024509273727
- 12 -0.72633938251319 -0.01122256237707 -0.01216129470990 0.00005391350069 -0.00022617397185 -0.00024509273727
- 13 0.72603838813733 0.01212691463322 0.01314129329840 -0.00008020751653 0.00022621309441 0.00024513514017
- 13 -0.72603838813732 -0.01212691463322 -0.01314129329840 0.00008020751653 -0.00022621309441 -0.00024513514017
- 14 0.72569772238094 0.01303226713237 0.01412237583128 -0.00007837151973 0.00022661957795 0.00024557563428
- 14 -0.72569772238093 -0.01303226713237 -0.01412237583128 0.00007837151973 -0.00022661957795 -0.00024557563428
- 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
- 16 0.72523999871705 0.01485059680662 0.01609280348805 -0.00002416178131 0.00022815395964 0.00024723838775
- 16 -0.72523999871704 -0.01485059680662 -0.01609280348805 0.00002416178131 -0.00022815395964 -0.00024723838775
- 17 0.72521812172908 0.01576510293390 0.01708380547460 0.00001507794579 0.00022913474609 0.00024830123034
- 17 -0.72521812172908 -0.01576510293391 -0.01708380547460 -0.00001507794579 -0.00022913474609 -0.00024830123034
- 18 0.72536062228341 0.01668367477532 0.01807921333078 0.00005625041435 0.00023014808425 0.00024939935061
- 18 -0.72536062228340 -0.01668367477532 -0.01807921333078 -0.00005625041435 -0.00023014808425 -0.00024939935061
- 19 0.72566812504388 0.01760628760793 0.01907900027949 0.00009650087857 0.00023114641406 0.00025048121053
- 19 -0.72566812504387 -0.01760628760793 -0.01907900027949 -0.00009650087857 -0.00023114641406 -0.00025048121053
- 20 0.72613262931195 0.01853284608778 0.02008306301505 0.00013403687154 0.00023209856863 0.00025151303647
- 20 -0.72613262931194 -0.01853284608778 -0.02008306301505 -0.00013403687154 -0.00023209856863 -0.00025151303647
- 21 0.72674042001620 0.01946307615693 0.02109110457125 0.00016766415629 0.00023295798887 0.00025244437542
- 21 -0.72674042001620 -0.01946307615693 -0.02109110457125 -0.00016766415629 -0.00023295798887 -0.00025244437542
- 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
- 23 0.72831423315702 0.02133271323312 0.02311713266083 0.00022098344374 0.00023433759982 0.00025393946265
- 23 -0.72831423315702 -0.02133271323312 -0.02311713266083 -0.00022098344374 -0.00023433759982 -0.00025393946265
- 24 0.72924181011222 0.02227121079730 0.02413413371961 0.00024032818130 0.00023483603069 0.00025447963179
- 24 -0.72924181011222 -0.02227121079730 -0.02413413371961 -0.00024032818130 -0.00023483603069 -0.00025447963179
- 25 0.73023685860739 0.02321140147860 0.02515296971514 0.00025481624125 0.00023519298119 0.00025486649200
- 25 -0.73023685860739 -0.02321140147860 -0.02515296971514 -0.00025481624125 -0.00023519298119 -0.00025486649200
- 26 0.73128034004219 0.02415275464679 0.02617306565557 0.00026467349225 0.00023542168715 0.00025511438699
- 26 -0.73128034004219 -0.02415275464680 -0.02617306565557 -0.00026467349225 -0.00023542168715 -0.00025511438699
- 27 0.73235424654535 0.02509477497584 0.02719388481103 0.00027010758805 0.00023551447637 0.00025521500303
- 27 -0.73235424654535 -0.02509477497584 -0.02719388481103 -0.00027010758805 -0.00023551447637 -0.00025521500303
- 28 0.73344120074658 0.02603687045779 0.02821478567984 0.00027134564227 0.00023546694185 0.00025516356438
- 28 -0.73344120074658 -0.02603687045779 -0.02821478567984 -0.00027134564227 -0.00023546694185 -0.00025516356438
- 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
- 30 0.73559077265617 0.02791923312252 0.03025460713037 0.00026241162068 0.00023499769277 0.00025465523294
- 30 -0.73559077265616 -0.02791923312252 -0.03025460713037 -0.00026241162068 -0.00023499769277 -0.00025465523294
- 31 0.73662430464896 0.02885849205281 0.03127243518962 0.00025272074446 0.00023456774370 0.00025418941566
- 31 -0.73662430464896 -0.02885849205281 -0.03127243518962 -0.00025272074446 -0.00023456774370 -0.00025418941566
- 32 0.73761253861181 0.02979577507214 0.03228812245563 0.00023992413820 0.00023402010459 0.00025359607392
- 32 -0.73761253861180 -0.02979577507214 -0.03228812245563 -0.00023992413820 -0.00023402010459 -0.00025359607392
- 33 0.73854369775457 0.03073065288949 0.03330120378100 0.00022427440798 0.00023335689709 0.00025287750774
- 33 -0.73854369775457 -0.03073065288950 -0.03330120378100 -0.00022427440798 -0.00023335689709 -0.00025287750774
- 34 0.73940673387562 0.03166263024882 0.03431114251756 0.00020599682177 0.00023257175449 0.00025202681362
- 34 -0.73940673387561 -0.03166263024882 -0.03431114251756 -0.00020599682177 -0.00023257175449 -0.00025202681362
- 35 0.74019167232872 0.03259122692542 0.03531741828998 0.00018541181754 0.00023167860378 0.00025105908813
- 35 -0.74019167232872 -0.03259122692542 -0.03531741828998 -0.00018541181754 -0.00023167860378 -0.00025105908813
- 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
- 37 0.74149444230477 0.03443672134444 0.03731729409361 0.00013864647024 0.00022959911555 0.00024880596230
- 37 -0.74149444230477 -0.03443672134444 -0.03731729409361 -0.00013864647024 -0.00022959911555 -0.00024880596230
- 38 0.74199920017784 0.03535285200351 0.03831006292093 0.00011333074516 0.00022843904823 0.00024754902429
- 38 -0.74199920017784 -0.03535285200351 -0.03831006292093 -0.00011333074516 -0.00022843904823 -0.00024754902429
- 39 0.74240108826605 0.03626423373030 0.03929768628789 0.00008747527307 0.00022723141891 0.00024624056979
- 39 -0.74240108826605 -0.03626423373031 -0.03929768628789 -0.00008747527307 -0.00022723141891 -0.00024624056979
- 40 0.74269900236237 0.03717070335480 0.04027998747923 0.00006153996769 0.00022599290438 0.00024489865284
- 40 -0.74269900236237 -0.03717070335480 -0.04027998747923 -0.00006153996769 -0.00022599290438 -0.00024489865284
- 41 0.74289340800760 0.03807217696532 0.04125687551058 0.00003585112144 0.00022474355412 0.00024354499486
- 41 -0.74289340800760 -0.03807217696533 -0.04125687551058 -0.00003585112144 -0.00022474355412 -0.00024354499486
- 42 0.74298581133387 0.03896865178777 0.04222834743813 0.00001048866569 0.00022348267808 0.00024217888239
- 42 -0.74298581133387 -0.03896865178777 -0.04222834743813 -0.00001048866569 -0.00022348267808 -0.00024217888239
- 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
- 44 0.74286781383868 0.04074621700688 0.04415462305260 -0.00004009642226 0.00022088100968 0.00023936007438
- 44 -0.74286781383868 -0.04074621700688 -0.04415462305261 0.00004009642226 -0.00022088100968 -0.00023936007438
- 45 0.74265654595502 0.04162708646738 0.04510918716471 -0.00006564676576 0.00021952106504 0.00023788664062
- 45 -0.74265654595502 -0.04162708646739 -0.04510918716471 0.00006564676576 -0.00021952106504 -0.00023788664062
- 46 0.74234263971264 0.04250238552716 0.04605771617754 -0.00009134238039 0.00021810231001 0.00023634953748
- 46 -0.74234263971264 -0.04250238552717 -0.04605771617754 0.00009134238039 -0.00021810231001 -0.00023634953748
- 47 0.74192580691191 0.04337190494748 0.04699998346457 -0.00011688598986 0.00021667055455 0.00023479831214
- 47 -0.74192580691191 -0.04337190494748 -0.04699998346457 0.00011688598986 -0.00021667055455 -0.00023479831214
- 48 0.74140755179378 0.04423574996358 0.04793610267467 -0.00014176306461 0.00021525878766 0.00023326873051
- 48 -0.74140755179378 -0.04423574996359 -0.04793610267468 0.00014176306461 -0.00021525878766 -0.00023326873051
- 49 0.74079170239500 0.04509397524877 0.04886613330868 -0.00016538618998 0.00021385628867 0.00023174930644
- 49 -0.74079170239500 -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
index 6fc12e118ffb5d28c1e98e28c0b7eac69d1788e7..c442d2456ff62e83804949876a299079f47c9296 100755
--- a/test/unittests/cpmd_4.1/md/nve/input.inp
+++ b/test/unittests/cpmd_4.1/md/nve/input.inp
@@ -12,7 +12,7 @@ simple molecular dynamics deltat=4au
50.0D0
MAXSTEP
- 50
+ 5
TIMESTEP
4.0
&END
diff --git a/test/unittests/cpmd_4.1/md/nve/output.out b/test/unittests/cpmd_4.1/md/nve/output.out
index b625a45fff05a02658c881cdd8fe97631662722b..dfd0bcc71d224df87dfabed431b4081142b4d450 100644
--- a/test/unittests/cpmd_4.1/md/nve/output.out
+++ b/test/unittests/cpmd_4.1/md/nve/output.out
@@ -1,5 +1,5 @@
cp_groups: we are using a 1 x 1 grid (groups x nprocs).
- PROGRAM CPMD STARTED AT: 2016-07-25 17:12:06.301
+ PROGRAM CPMD STARTED AT: 2016-07-27 13:27:37.467
SETCNST| USING: CODATA 2006 UNITS
@@ -32,7 +32,7 @@
/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 PROCESS ID IS: 9982
THE JOB WAS SUBMITTED BY: lauri
@@ -50,7 +50,7 @@
ITERATIVE ORTHOGONALIZATION
MAXIT: 30
EPS: 1.00E-06
- MAXIMUM NUMBER OF STEPS: 50 STEPS
+ MAXIMUM NUMBER OF STEPS: 5 STEPS
MAXIMUM NUMBER OF ITERATIONS FOR SC: 10000 STEPS
PRINT INTERMEDIATE RESULTS EVERY 10001 STEPS
STORE INTERMEDIATE RESULTS EVERY 10001 STEPS
@@ -154,7 +154,7 @@
1S ALPHA= 1.0000 OCCUPATION= 1.00
- INITIALIZATION TIME: 0.48 SECONDS
+ INITIALIZATION TIME: 0.49 SECONDS
*** MDPT| SIZE OF THE PROGRAM IS NOT AVAILABLE ***
*** PHFAC| SIZE OF THE PROGRAM IS NOT AVAILABLE ***
@@ -189,7 +189,7 @@
== END OF FORCES INITIALIZATION ==
================================================================
- TIME FOR INITIALIZATION: 1.07 SECONDS
+ TIME FOR INITIALIZATION: 1.09 SECONDS
****************************************************************
* ATOMIC COORDINATES *
@@ -213,56 +213,11 @@
(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
+ 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 0.24
+ 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 0.24
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
@@ -271,17 +226,17 @@
****************************************************************
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
+ ELECTRON KINETIC ENERGY 0.018451 0.800503E-02
+ IONIC TEMPERATURE 300.0613 113.733
+ DENSITY FUNCTIONAL ENERGY -1.117412 0.876222E-02
+ CLASSICAL ENERGY -1.115986 0.822265E-02
+ CONSERVED ENERGY -1.097536 0.234060E-03
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
+ ION DISPLACEMENT 0.940474E-04 0.917156E-04
+ CPU TIME 0.2370
****************************************************************
* *
@@ -292,8 +247,8 @@
****************************************************************
* ATOMIC COORDINATES *
****************************************************************
- 1 H 0.740084 0.045947 0.049790
- 2 H -0.740084 -0.045947 -0.049790
+ 1 H 0.715305 0.004785 0.005186
+ 2 H -0.715305 -0.004785 -0.005186
****************************************************************
@@ -301,20 +256,20 @@
ELECTRONIC GRADIENT:
- MAX. COMPONENT = 1.39929E-02 NORM = 2.08955E-03
+ MAX. COMPONENT = 7.46544E-03 NORM = 1.85389E-03
TOTAL INTEGRATED ELECTRONIC DENSITY
- IN G-SPACE = 1.9999999999
- IN R-SPACE = 1.9999999999
+ IN G-SPACE = 1.9999999998
+ IN R-SPACE = 1.9999999998
- (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.
+ (K+E1+L+N+X) TOTAL ENERGY = -1.12453355 A.U.
+ (K) KINETIC ENERGY = 1.11789875 A.U.
+ (E1=A-S+R) ELECTROSTATIC ENERGY = -0.47871616 A.U.
(S) ESELF = 0.66490380 A.U.
- (R) ESR = 0.14497305 A.U.
- (L) LOCAL PSEUDOPOTENTIAL ENERGY = -1.04064388 A.U.
+ (R) ESR = 0.16297859 A.U.
+ (L) LOCAL PSEUDOPOTENTIAL ENERGY = -1.11784096 A.U.
(N) N-L PSEUDOPOTENTIAL ENERGY = 0.00000000 A.U.
- (X) EXCHANGE-CORRELATION ENERGY = -0.63585977 A.U.
+ (X) EXCHANGE-CORRELATION ENERGY = -0.64587518 A.U.
****************************************************************
@@ -327,48 +282,47 @@
****************************************************************
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
+ cpmd 1 0.01 0.01 2.76 2.76
+ mdpt 1 0.00 0.00 2.28 2.28
+ mdmain 1 0.00 0.00 2.28 2.28
+ forcedr 6 0.00 0.00 1.42 1.42
+ forces 6 0.00 0.00 1.42 1.42
+ vofrho 7 0.00 0.00 1.25 1.25
+ forces_a 6 0.00 0.00 1.11 1.11
+ rscpot 6 0.00 0.00 1.11 1.11
+ initrun 1 0.00 0.00 0.85 0.85
+ rinitwf 1 0.00 0.00 0.85 0.85
+ ATOMWF 1 0.00 0.00 0.85 0.85
+ VOFRHOB 7 0.03 0.03 0.85 0.85
+ INVFFTN 22 0.72 0.72 0.72 0.72
+ xcener_new 7 0.03 0.03 0.48 0.48
+ mikeu 7 0.46 0.46 0.46 0.46
+ FWFFTN 15 0.42 0.42 0.42 0.42
+ ATRHO 1 0.38 0.38 0.42 0.42
+ vpsi 8 0.04 0.04 0.40 0.40
+ VOFRHOA 7 0.02 0.02 0.40 0.40
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
+ loadpa 1 0.01 0.01 0.25 0.25
+ rhoofr 6 0.04 0.04 0.19 0.19
+ RINFORCE 1 0.00 0.00 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
- 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
+ loadpa_c 1 0.09 0.09 0.09 0.09
+ potfor 6 0.06 0.06 0.06 0.06
+ loadpa_a 1 0.04 0.04 0.04 0.04
+ ppener 7 0.04 0.04 0.04 0.04
+ EICALC 7 0.03 0.03 0.03 0.03
+ PUTPS 1 0.01 0.01 0.01 0.01
+ fftprp 1 0.00 0.00 0.00 0.00
+ PHFAC 6 0.00 0.00 0.00 0.00
+ forces_b 6 0.00 0.00 0.00 0.00
****************************************************************
- CPU TIME : 0 HOURS 0 MINUTES 13.36 SECONDS
- ELAPSED TIME : 0 HOURS 0 MINUTES 13.37 SECONDS
+ CPU TIME : 0 HOURS 0 MINUTES 2.75 SECONDS
+ ELAPSED TIME : 0 HOURS 0 MINUTES 2.77 SECONDS
*** CPMD| SIZE OF THE PROGRAM IS NOT AVAILABLE ***
- PROGRAM CPMD ENDED AT: 2016-07-25 17:12:19.667
+ PROGRAM CPMD ENDED AT: 2016-07-27 13:27:40.229
diff --git a/test/unittests/cpmd_4.1/md/trajectory/ENERGIES b/test/unittests/cpmd_4.1/md/trajectory/ENERGIES
new file mode 100644
index 0000000000000000000000000000000000000000..6be0122a160036c44a90402694fdd8915431dddc
--- /dev/null
+++ b/test/unittests/cpmd_4.1/md/trajectory/ENERGIES
@@ -0,0 +1,5 @@
+ 1 0.00472945 110.096 -1.1023492072 -1.1018262261 -1.0970967730 0.288545E-05 0.27
+ 2 0.01424065 232.496 -1.1128688938 -1.1117644858 -1.0975238350 0.182162E-04 0.27
+ 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
diff --git a/test/unittests/cpmd_4.1/md/trajectory/GEOMETRY b/test/unittests/cpmd_4.1/md/trajectory/GEOMETRY
new file mode 100644
index 0000000000000000000000000000000000000000..5209a7da40841355f0f4a8ebe66f3f6b212e2da1
--- /dev/null
+++ b/test/unittests/cpmd_4.1/md/trajectory/GEOMETRY
@@ -0,0 +1,2 @@
+ 0.715304751615 0.004785368892 0.005185649980 0.000946442689 0.000235633854 0.000255343887
+ -0.715304751615 -0.004785368892 -0.005185649980 -0.000946442689 -0.000235633854 -0.000255343887
diff --git a/test/unittests/cpmd_4.1/md/trajectory/GEOMETRY.xyz b/test/unittests/cpmd_4.1/md/trajectory/GEOMETRY.xyz
new file mode 100644
index 0000000000000000000000000000000000000000..644d2c0c17085461cbc66efb46bfc7ea7b45720e
--- /dev/null
+++ b/test/unittests/cpmd_4.1/md/trajectory/GEOMETRY.xyz
@@ -0,0 +1,4 @@
+ 2
+GEOMETRY FILE / created by CPMD
+ H 0.378522973374 0.002532308163 0.002744127793 0.000500835903 0.000124692066 0.000135122166
+ H -0.378522973374 -0.002532308163 -0.002744127793 -0.000500835903 -0.000124692066 -0.000135122166
diff --git a/test/unittests/cpmd_4.1/md/trajectory/LATEST b/test/unittests/cpmd_4.1/md/trajectory/LATEST
new file mode 100644
index 0000000000000000000000000000000000000000..0e4449210602fd9c3a45bd3bc780cd67ad8721b0
--- /dev/null
+++ b/test/unittests/cpmd_4.1/md/trajectory/LATEST
@@ -0,0 +1,2 @@
+./RESTART.1
+ 1
diff --git a/test/unittests/cpmd_4.1/md/trajectory/RESTART.1 b/test/unittests/cpmd_4.1/md/trajectory/RESTART.1
new file mode 100644
index 0000000000000000000000000000000000000000..27a03a7f2a45e0aefb9112ae2a5ca61b396f2e9b
Binary files /dev/null and b/test/unittests/cpmd_4.1/md/trajectory/RESTART.1 differ
diff --git a/test/unittests/cpmd_4.1/md/trajectory/TRAJECTORY b/test/unittests/cpmd_4.1/md/trajectory/TRAJECTORY
new file mode 100644
index 0000000000000000000000000000000000000000..a2177c5422573451e5a04350da1e8d13bc79a8ed
--- /dev/null
+++ b/test/unittests/cpmd_4.1/md/trajectory/TRAJECTORY
@@ -0,0 +1,10 @@
+ 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
+ 2 0.70427017594465 0.00192922057414 0.00209059381907 0.00068971096691 0.00024011990909 0.00026020518573
+ 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
+ 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
+ 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
+ 5 -0.71530475161473 -0.00478536889215 -0.00518564998016 -0.00094644268934 -0.00023563385430 -0.00025534388718
diff --git a/test/unittests/cpmd_4.1/md/trajectory/input.inp b/test/unittests/cpmd_4.1/md/trajectory/input.inp
new file mode 100755
index 0000000000000000000000000000000000000000..d192015aca193c6d7c60f41d0d177a40e41f714d
--- /dev/null
+++ b/test/unittests/cpmd_4.1/md/trajectory/input.inp
@@ -0,0 +1,41 @@
+&INFO
+isolated hydrogen molecule.
+simple molecular dynamics deltat=4au
+&END
+
+&CPMD
+ MOLECULAR DYNAMICS CP
+
+ TRAJECTORY
+
+ TEMPERATURE
+ 50.0D0
+
+ MAXSTEP
+ 5
+ 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/trajectory/output.out b/test/unittests/cpmd_4.1/md/trajectory/output.out
new file mode 100644
index 0000000000000000000000000000000000000000..7a81481c853cd34dadbd03d77a990d30f3d89621
--- /dev/null
+++ b/test/unittests/cpmd_4.1/md/trajectory/output.out
@@ -0,0 +1,327 @@
+ cp_groups: we are using a 1 x 1 grid (groups x nprocs).
+ PROGRAM CPMD STARTED AT: 2016-07-27 18:34:54.220
+ 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/trajectory
+ THE TEMPORARY DIRECTORY IS:
+ /home/lauri/Dropbox/nomad-dev/nomad-lab-base/parsers/cpmd/test/unittests/cpmd_4.1/md/trajectory
+ THE PROCESS ID IS: 24185
+ 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: 5 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
+ 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: 1.14 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 0.27
+ 2 0.01424 232.5 -1.11287 -1.11176 -1.09752 0.182E-04 0.27
+ 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
+
+ RESTART INFORMATION WRITTEN ON FILE ./RESTART.1
+
+ ****************************************************************
+ * AVERAGED QUANTITIES *
+ ****************************************************************
+ MEAN VALUE +/- RMS DEVIATION
+ <x> [<x^2>-<x>^2]**(1/2)
+ ELECTRON KINETIC ENERGY 0.018451 0.800503E-02
+ IONIC TEMPERATURE 300.0613 113.733
+ DENSITY FUNCTIONAL ENERGY -1.117412 0.876222E-02
+ CLASSICAL ENERGY -1.115986 0.822265E-02
+ CONSERVED ENERGY -1.097536 0.234060E-03
+ 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 0.940474E-04 0.917156E-04
+ CPU TIME 0.2492
+
+ ****************************************************************
+ * *
+ * FINAL RESULTS *
+ * *
+ ****************************************************************
+
+ ****************************************************************
+ * ATOMIC COORDINATES *
+ ****************************************************************
+ 1 H 0.715305 0.004785 0.005186
+ 2 H -0.715305 -0.004785 -0.005186
+ ****************************************************************
+
+
+ ****************************************************************
+
+
+ ELECTRONIC GRADIENT:
+ MAX. COMPONENT = 7.46544E-03 NORM = 1.85389E-03
+
+ TOTAL INTEGRATED ELECTRONIC DENSITY
+ IN G-SPACE = 1.9999999998
+ IN R-SPACE = 1.9999999998
+
+ (K+E1+L+N+X) TOTAL ENERGY = -1.12453355 A.U.
+ (K) KINETIC ENERGY = 1.11789875 A.U.
+ (E1=A-S+R) ELECTROSTATIC ENERGY = -0.47871616 A.U.
+ (S) ESELF = 0.66490380 A.U.
+ (R) ESR = 0.16297859 A.U.
+ (L) LOCAL PSEUDOPOTENTIAL ENERGY = -1.11784096 A.U.
+ (N) N-L PSEUDOPOTENTIAL ENERGY = 0.00000000 A.U.
+ (X) EXCHANGE-CORRELATION ENERGY = -0.64587518 A.U.
+
+ ****************************************************************
+
+
+
+ ****************************************************************
+ * *
+ * TIMING *
+ * *
+ ****************************************************************
+ SUBROUTINE CALLS SELF TIME TOTAL TIME
+ AVERAGE MAXIMUM AVERAGE MAXIMUM
+ cpmd 1 0.01 0.01 2.89 2.89
+ mdpt 1 0.00 0.00 2.39 2.39
+ mdmain 1 0.00 0.00 2.39 2.39
+ forcedr 6 0.00 0.00 1.50 1.50
+ forces 6 0.00 0.00 1.50 1.50
+ vofrho 7 0.00 0.00 1.31 1.31
+ forces_a 6 0.00 0.00 1.18 1.18
+ rscpot 6 0.00 0.00 1.18 1.18
+ VOFRHOB 7 0.03 0.03 0.90 0.90
+ initrun 1 0.00 0.00 0.88 0.88
+ rinitwf 1 0.00 0.00 0.88 0.88
+ ATOMWF 1 0.00 0.00 0.88 0.88
+ INVFFTN 22 0.78 0.78 0.78 0.78
+ xcener_new 7 0.03 0.03 0.51 0.51
+ mikeu 7 0.48 0.48 0.48 0.48
+ FWFFTN 15 0.45 0.45 0.45 0.45
+ vpsi 8 0.04 0.04 0.44 0.44
+ ATRHO 1 0.38 0.38 0.42 0.42
+ VOFRHOA 7 0.02 0.02 0.41 0.41
+ rinit 1 0.00 0.00 0.27 0.27
+ rggen 1 0.01 0.01 0.27 0.27
+ loadpa 1 0.01 0.01 0.26 0.26
+ rhoofr 6 0.04 0.04 0.21 0.21
+ dist_ksmat 1 0.00 0.00 0.12 0.12
+ loadpa_b 1 0.11 0.11 0.11 0.11
+ NUMPW 1 0.10 0.10 0.10 0.10
+ RINFORCE 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
+ potfor 6 0.06 0.06 0.06 0.06
+ loadpa_a 1 0.05 0.05 0.05 0.05
+ ppener 7 0.05 0.05 0.05 0.05
+ EICALC 7 0.03 0.03 0.03 0.03
+ fftprp 1 0.01 0.01 0.01 0.01
+ PUTPS 1 0.01 0.01 0.01 0.01
+ ROTATE 17 0.00 0.00 0.00 0.00
+ POSUPA 5 0.00 0.00 0.00 0.00
+ ****************************************************************
+
+ CPU TIME : 0 HOURS 0 MINUTES 2.89 SECONDS
+ ELAPSED TIME : 0 HOURS 0 MINUTES 2.89 SECONDS
+ *** CPMD| SIZE OF THE PROGRAM IS NOT AVAILABLE ***
+
+ PROGRAM CPMD ENDED AT: 2016-07-27 18:34:57.110
diff --git a/test/unittests/cpmd_4.1/md/trajectory/run.sh b/test/unittests/cpmd_4.1/md/trajectory/run.sh
new file mode 100755
index 0000000000000000000000000000000000000000..74ce0ca5a55a21a25741d586bcf4cb42c8f14590
--- /dev/null
+++ b/test/unittests/cpmd_4.1/md/trajectory/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/ENERGIES b/test/unittests/cpmd_4.1/md/xyz/ENERGIES
new file mode 100644
index 0000000000000000000000000000000000000000..df4e9d3f709cc3d6c4fcb6f5df567b84e761ca52
--- /dev/null
+++ b/test/unittests/cpmd_4.1/md/xyz/ENERGIES
@@ -0,0 +1,5 @@
+ 1 0.00472945 110.096 -1.1023492072 -1.1018262261 -1.0970967730 0.288545E-05 0.32
+ 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 0.24
+ 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 0.25
diff --git a/test/unittests/cpmd_4.1/md/xyz/GEOMETRY b/test/unittests/cpmd_4.1/md/xyz/GEOMETRY
new file mode 100644
index 0000000000000000000000000000000000000000..5209a7da40841355f0f4a8ebe66f3f6b212e2da1
--- /dev/null
+++ b/test/unittests/cpmd_4.1/md/xyz/GEOMETRY
@@ -0,0 +1,2 @@
+ 0.715304751615 0.004785368892 0.005185649980 0.000946442689 0.000235633854 0.000255343887
+ -0.715304751615 -0.004785368892 -0.005185649980 -0.000946442689 -0.000235633854 -0.000255343887
diff --git a/test/unittests/cpmd_4.1/md/xyz/GEOMETRY.xyz b/test/unittests/cpmd_4.1/md/xyz/GEOMETRY.xyz
new file mode 100644
index 0000000000000000000000000000000000000000..644d2c0c17085461cbc66efb46bfc7ea7b45720e
--- /dev/null
+++ b/test/unittests/cpmd_4.1/md/xyz/GEOMETRY.xyz
@@ -0,0 +1,4 @@
+ 2
+GEOMETRY FILE / created by CPMD
+ H 0.378522973374 0.002532308163 0.002744127793 0.000500835903 0.000124692066 0.000135122166
+ H -0.378522973374 -0.002532308163 -0.002744127793 -0.000500835903 -0.000124692066 -0.000135122166
diff --git a/test/unittests/cpmd_4.1/md/xyz/LATEST b/test/unittests/cpmd_4.1/md/xyz/LATEST
new file mode 100644
index 0000000000000000000000000000000000000000..0e4449210602fd9c3a45bd3bc780cd67ad8721b0
--- /dev/null
+++ b/test/unittests/cpmd_4.1/md/xyz/LATEST
@@ -0,0 +1,2 @@
+./RESTART.1
+ 1
diff --git a/test/unittests/cpmd_4.1/md/xyz/RESTART.1 b/test/unittests/cpmd_4.1/md/xyz/RESTART.1
new file mode 100644
index 0000000000000000000000000000000000000000..b14f47d353dda2ed09b5a919de8df8e9766c436f
Binary files /dev/null and b/test/unittests/cpmd_4.1/md/xyz/RESTART.1 differ
diff --git a/test/unittests/cpmd_4.1/md/xyz/TRAJEC.xyz b/test/unittests/cpmd_4.1/md/xyz/TRAJEC.xyz
new file mode 100644
index 0000000000000000000000000000000000000000..fee8c8bf77f773de37d0a9814c1e80b2ac365089
--- /dev/null
+++ b/test/unittests/cpmd_4.1/md/xyz/TRAJEC.xyz
@@ -0,0 +1,20 @@
+ 2
+ STEP: 1
+ H 0.371489 0.000511 0.000554
+ H -0.371489 -0.000511 -0.000554
+ 2
+ STEP: 2
+ H 0.372684 0.001021 0.001106
+ H -0.372684 -0.001021 -0.001106
+ 2
+ STEP: 3
+ H 0.374409 0.001528 0.001656
+ H -0.374409 -0.001528 -0.001656
+ 2
+ STEP: 4
+ H 0.376437 0.002032 0.002202
+ H -0.376437 -0.002032 -0.002202
+ 2
+ STEP: 5
+ H 0.378523 0.002532 0.002744
+ H -0.378523 -0.002532 -0.002744
diff --git a/test/unittests/cpmd_4.1/md/xyz/TRAJECTORY b/test/unittests/cpmd_4.1/md/xyz/TRAJECTORY
new file mode 100644
index 0000000000000000000000000000000000000000..a2177c5422573451e5a04350da1e8d13bc79a8ed
--- /dev/null
+++ b/test/unittests/cpmd_4.1/md/xyz/TRAJECTORY
@@ -0,0 +1,10 @@
+ 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
+ 2 0.70427017594465 0.00192922057414 0.00209059381907 0.00068971096691 0.00024011990909 0.00026020518573
+ 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
+ 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
+ 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
+ 5 -0.71530475161473 -0.00478536889215 -0.00518564998016 -0.00094644268934 -0.00023563385430 -0.00025534388718
diff --git a/test/unittests/cpmd_4.1/md/xyz/input.inp b/test/unittests/cpmd_4.1/md/xyz/input.inp
index 6fc12e118ffb5d28c1e98e28c0b7eac69d1788e7..c442d2456ff62e83804949876a299079f47c9296 100755
--- a/test/unittests/cpmd_4.1/md/xyz/input.inp
+++ b/test/unittests/cpmd_4.1/md/xyz/input.inp
@@ -12,7 +12,7 @@ simple molecular dynamics deltat=4au
50.0D0
MAXSTEP
- 50
+ 5
TIMESTEP
4.0
&END
diff --git a/test/unittests/cpmd_4.1/md/xyz/output.out b/test/unittests/cpmd_4.1/md/xyz/output.out
new file mode 100644
index 0000000000000000000000000000000000000000..b1e33038d82a854d4af1ed0be96706d0323e8945
--- /dev/null
+++ b/test/unittests/cpmd_4.1/md/xyz/output.out
@@ -0,0 +1,329 @@
+ cp_groups: we are using a 1 x 1 grid (groups x nprocs).
+ PROGRAM CPMD STARTED AT: 2016-07-27 18:33:20.444
+ 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/xyz
+ THE TEMPORARY DIRECTORY IS:
+ /home/lauri/Dropbox/nomad-dev/nomad-lab-base/parsers/cpmd/test/unittests/cpmd_4.1/md/xyz
+ THE PROCESS ID IS: 23930
+ 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: 5 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: 0.52 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 0.32
+ 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 0.24
+ 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 0.25
+
+ RESTART INFORMATION WRITTEN ON FILE ./RESTART.1
+
+ ****************************************************************
+ * AVERAGED QUANTITIES *
+ ****************************************************************
+ MEAN VALUE +/- RMS DEVIATION
+ <x> [<x^2>-<x>^2]**(1/2)
+ ELECTRON KINETIC ENERGY 0.018451 0.800503E-02
+ IONIC TEMPERATURE 300.0613 113.733
+ DENSITY FUNCTIONAL ENERGY -1.117412 0.876222E-02
+ CLASSICAL ENERGY -1.115986 0.822265E-02
+ CONSERVED ENERGY -1.097536 0.234060E-03
+ 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 0.940474E-04 0.917156E-04
+ CPU TIME 0.2594
+
+ ****************************************************************
+ * *
+ * FINAL RESULTS *
+ * *
+ ****************************************************************
+
+ ****************************************************************
+ * ATOMIC COORDINATES *
+ ****************************************************************
+ 1 H 0.715305 0.004785 0.005186
+ 2 H -0.715305 -0.004785 -0.005186
+ ****************************************************************
+
+
+ ****************************************************************
+
+
+ ELECTRONIC GRADIENT:
+ MAX. COMPONENT = 7.46544E-03 NORM = 1.85389E-03
+
+ TOTAL INTEGRATED ELECTRONIC DENSITY
+ IN G-SPACE = 1.9999999998
+ IN R-SPACE = 1.9999999998
+
+ (K+E1+L+N+X) TOTAL ENERGY = -1.12453355 A.U.
+ (K) KINETIC ENERGY = 1.11789875 A.U.
+ (E1=A-S+R) ELECTROSTATIC ENERGY = -0.47871616 A.U.
+ (S) ESELF = 0.66490380 A.U.
+ (R) ESR = 0.16297859 A.U.
+ (L) LOCAL PSEUDOPOTENTIAL ENERGY = -1.11784096 A.U.
+ (N) N-L PSEUDOPOTENTIAL ENERGY = 0.00000000 A.U.
+ (X) EXCHANGE-CORRELATION ENERGY = -0.64587518 A.U.
+
+ ****************************************************************
+
+
+
+ ****************************************************************
+ * *
+ * TIMING *
+ * *
+ ****************************************************************
+ SUBROUTINE CALLS SELF TIME TOTAL TIME
+ AVERAGE MAXIMUM AVERAGE MAXIMUM
+ cpmd 1 0.01 0.01 2.94 2.94
+ mdpt 1 0.00 0.00 2.42 2.42
+ mdmain 1 0.00 0.00 2.42 2.42
+ forcedr 6 0.00 0.00 1.54 1.54
+ forces 6 0.00 0.00 1.54 1.54
+ vofrho 7 0.00 0.00 1.34 1.34
+ forces_a 6 0.00 0.00 1.21 1.21
+ rscpot 6 0.00 0.00 1.21 1.21
+ VOFRHOB 7 0.03 0.03 0.88 0.88
+ initrun 1 0.00 0.00 0.87 0.87
+ rinitwf 1 0.00 0.00 0.87 0.87
+ ATOMWF 1 0.00 0.00 0.87 0.87
+ INVFFTN 22 0.76 0.76 0.76 0.76
+ xcener_new 7 0.03 0.03 0.51 0.51
+ FWFFTN 15 0.49 0.49 0.49 0.49
+ mikeu 7 0.48 0.48 0.48 0.48
+ VOFRHOA 7 0.02 0.02 0.46 0.46
+ vpsi 8 0.04 0.04 0.43 0.43
+ ATRHO 1 0.38 0.38 0.42 0.42
+ 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
+ rhoofr 6 0.05 0.05 0.22 0.22
+ NUMPW 1 0.11 0.11 0.11 0.11
+ RINFORCE 1 0.00 0.00 0.11 0.11
+ FORMFN 1 0.10 0.10 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
+ loadpa_c 1 0.10 0.10 0.10 0.10
+ potfor 6 0.07 0.07 0.07 0.07
+ loadpa_a 1 0.04 0.04 0.04 0.04
+ ppener 7 0.04 0.04 0.04 0.04
+ EICALC 7 0.03 0.03 0.03 0.03
+ fftprp 1 0.01 0.01 0.01 0.01
+ PUTPS 1 0.01 0.01 0.01 0.01
+ POSUPA 5 0.00 0.00 0.00 0.00
+ ROTATE 17 0.00 0.00 0.00 0.00
+ RORTOG 5 0.00 0.00 0.00 0.00
+ ****************************************************************
+
+ CPU TIME : 0 HOURS 0 MINUTES 2.94 SECONDS
+ ELAPSED TIME : 0 HOURS 0 MINUTES 2.94 SECONDS
+ *** CPMD| SIZE OF THE PROGRAM IS NOT AVAILABLE ***
+
+ PROGRAM CPMD ENDED AT: 2016-07-27 18:33:23.382
diff --git a/test/unittests/cpmd_4.1/run_tests.py b/test/unittests/cpmd_4.1/run_tests.py
index 15bc9ee91799f44d4fe3b49b031cc849ed15ab6c..9178139284edaf9b1b8e33e1cb9c20492eee514b 100644
--- a/test/unittests/cpmd_4.1/run_tests.py
+++ b/test/unittests/cpmd_4.1/run_tests.py
@@ -385,72 +385,55 @@ class TestMD(unittest.TestCase):
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,
+ 110.096,
+ 232.496,
+ 351.956,
+ 412.578,
+ 393.180,
]),
"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,
+ -1.0970967730,
+ -1.0975238350,
+ -1.0977293448,
+ -1.0977368045,
+ -1.0975921059,
]),
"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,
+ -1.1023492072,
+ -1.1128688938,
+ -1.1216882365,
+ -1.1256188624,
+ -1.1245335482,
]),
"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,
+ -1.1018262261,
+ -1.1117644858,
+ -1.1200163669,
+ -1.1236590243,
+ -1.1226658551,
+ ]) -
+ np.array([
+ -1.1023492072,
+ -1.1128688938,
+ -1.1216882365,
+ -1.1256188624,
+ -1.1245335482,
]),
"hartree"
)
def test_number_of_atoms(self):
result = self.results["number_of_atoms"]
- expected_result = np.array(50*[2])
+ expected_result = np.array(5*[2])
self.assertTrue(np.array_equal(result, expected_result))
def test_ensemble_type(self):
@@ -463,7 +446,7 @@ class TestMD(unittest.TestCase):
def test_number_of_frames_in_sequence(self):
result = self.results["number_of_frames_in_sequence"]
- self.assertEqual(result, 50)
+ self.assertEqual(result, 5)
def test_atom_positions(self):
result = self.results["atom_positions"]
@@ -476,97 +459,151 @@ class TestMD(unittest.TestCase):
)
expected_end = convert_unit(
np.array([
- [0.391636, 0.024314, 0.026348],
- [-0.391636, -0.024314, -0.026348],
+ [0.378523, 0.002532, 0.002744],
+ [-0.378523, -0.002532, -0.002744],
]),
"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"
- # )
+ def test_atom_velocities(self):
+ result = self.results["atom_velocities"]
+ expected_start = convert_unit(
+ np.array([
+ [0.00039772295627, 0.00024115257177, 0.00026132422738],
+ [-0.00039772295627, -0.00024115257177, -0.00026132422738],
+ ]),
+ "bohr/(hbar/hartree)"
+ )
+ expected_end = convert_unit(
+ np.array([
+ [0.00094644268934, 0.00023563385430, 0.00025534388718],
+ [-0.00094644268934, -0.00023563385430, -0.00025534388718],
+ ]),
+ "bohr/(hbar/hartree)"
+ )
- # self.assertTrue(np.array_equal(result[0,:], expected_start))
- # self.assertTrue(np.array_equal(result[-1,:], expected_end))
+ 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_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_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_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_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_time(self):
+ result = self.results["frame_sequence_time"]
+ expected_result = convert_unit(
+ np.array([
+ 4,
+ 8,
+ 12,
+ 16,
+ 20,
+ ]),
+ "hbar/hartree"
+ )
+ 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_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.allclose(result[0], expected_result[0], rtol=0, atol=0.00001e-18))
+ self.assertTrue(np.allclose(result[1], expected_result[1], rtol=0, atol=0.00001e-20))
- # 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_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.allclose(result[0], expected_result[0], rtol=0, atol=0.00001e-18))
+ self.assertTrue(np.allclose(result[1], expected_result[1], rtol=0, atol=0.00001e-20))
- # 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_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.allclose(result[0], expected_result[0], rtol=0, atol=0.00001e-18))
+ self.assertTrue(np.allclose(result[1], expected_result[1], rtol=0, atol=0.00001e-20))
- # 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))
+ 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.allclose(result[0], expected_result[0], rtol=0, atol=0.001))
+ self.assertTrue(np.allclose(result[1], expected_result[1], rtol=0, atol=0.0001))
+
+
+#===============================================================================
+class TestMDTrajFormats(unittest.TestCase):
+
+ def test_dcd(self):
+ results = get_results("md/dcd", "section_run")
+ positions = results["atom_positions"]
+ expected_start = convert_unit(
+ np.array([
+ [0.70201340784773, 0.00096620207776, 0.00104702184853],
+ [-0.70201340784773, -0.00096620207776, -0.00104702184853],
+ ]),
+ "bohr"
+ )
+ expected_end = convert_unit(
+ np.array([
+ [0.71530475161473, 0.00478536889215, 0.00518564998016],
+ [-0.71530475161473, -0.00478536889215, -0.00518564998016],
+ ]),
+ "bohr"
+ )
+ self.assertTrue(np.allclose(positions[0, :], expected_start, rtol=0, atol=0.0000001e-11))
+ self.assertTrue(np.allclose(positions[-1, :], expected_end, rtol=0, atol=0.0000001e-11))
+
+ def test_xyz(self):
+ results = get_results("md/xyz", "section_run")
+ positions = results["atom_positions"]
+ expected_start = convert_unit(
+ np.array([
+ [0.70201340784773, 0.00096620207776, 0.00104702184853],
+ [-0.70201340784773, -0.00096620207776, -0.00104702184853],
+ ]),
+ "bohr"
+ )
+ expected_end = convert_unit(
+ np.array([
+ [0.71530475161473, 0.00478536889215, 0.00518564998016],
+ [-0.71530475161473, -0.00478536889215, -0.00518564998016],
+ ]),
+ "bohr"
+ )
+ self.assertTrue(np.allclose(positions[0, :], expected_start, rtol=0, atol=0.00001e-11))
+ self.assertTrue(np.allclose(positions[-1, :], expected_end, rtol=0, atol=0.00001e-11))
+
+ def test_trajectory(self):
+ results = get_results("md/trajectory", "section_run")
+ positions = results["atom_positions"]
+ expected_start = convert_unit(
+ np.array([
+ [0.70201340784773, 0.00096620207776, 0.00104702184853],
+ [-0.70201340784773, -0.00096620207776, -0.00104702184853],
+ ]),
+ "bohr"
+ )
+ expected_end = convert_unit(
+ np.array([
+ [0.71530475161473, 0.00478536889215, 0.00518564998016],
+ [-0.71530475161473, -0.00478536889215, -0.00518564998016],
+ ]),
+ "bohr"
+ )
+ self.assertTrue(np.allclose(positions[0, :], expected_start, rtol=0, atol=0.00001e-11))
+ self.assertTrue(np.allclose(positions[-1, :], expected_end, rtol=0, atol=0.00001e-11))
# #===============================================================================
@@ -1034,9 +1071,10 @@ class TestMD(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))
+ suites.append(unittest.TestLoader().loadTestsFromTestCase(TestMDTrajFormats))
alltests = unittest.TestSuite(suites)
unittest.TextTestRunner(verbosity=0).run(alltests)