diff --git a/parser/parser-cpmd/cpmdparser/versions/cpmd41/inputparser.py b/parser/parser-cpmd/cpmdparser/versions/cpmd41/inputparser.py index 9805eab50a6b6a7db3f18953577f66b7bd78a519..7f22bf9344da4655480a2c4cd542ae94926b4104 100644 --- a/parser/parser-cpmd/cpmdparser/versions/cpmd41/inputparser.py +++ b/parser/parser-cpmd/cpmdparser/versions/cpmd41/inputparser.py @@ -15,10 +15,14 @@ class CPMDInputParser(BasicParser): """ super(CPMDInputParser, self).__init__(file_path, parser_context) self.input_tree = None + self.cache_service.add("trajectory_range", False) + self.cache_service.add("trajectory_sample", False) + self.cache_service.add("print_freq", 1) def parse(self): self.setup_input_tree(self.parser_context.version_id) self.collect_input() + self.analyze_input() self.fill_metadata() def collect_input(self): @@ -109,6 +113,27 @@ class CPMDInputParser(BasicParser): if keyword_object is None: parameters.append(line) + def analyze_input(self): + # Get the trajectory print settings + root = self.input_tree + cpmd = root.get_section("CPMD") + trajectory = cpmd.get_keyword("TRAJECTORY") + if trajectory: + options = trajectory.options + if options: + if "RANGE" in options: + self.cache_service["trajectory_range"] = True + if "SAMPLE" in options: + self.cache_service["trajectory_sample"] = True + parameters = trajectory.parameters + try: + lines = parameters.split("\n") + print_freq = int(lines[-1]) + except (IndexError, ValueError): + self.cache_service["print_freq"] = None + else: + self.cache_service["print_freq"] = print_freq + def fill_metadata(self): """Goes through the input data and pushes everything to the backend. diff --git a/parser/parser-cpmd/cpmdparser/versions/cpmd41/mdparser.py b/parser/parser-cpmd/cpmdparser/versions/cpmd41/mdparser.py index b11d1d5c4bebb647f3b10447d8f875781e8f7872..2cdc631e4327c77b7f768418afe1fdb9977f0d55 100644 --- a/parser/parser-cpmd/cpmdparser/versions/cpmd41/mdparser.py +++ b/parser/parser-cpmd/cpmdparser/versions/cpmd41/mdparser.py @@ -110,6 +110,11 @@ class CPMDMDParser(MainHierarchicalParser): """Parses all the md step information. """ # Decide from which file trajectory is read + n_atoms = self.cache_service["number_of_atoms"] + trajectory_range = self.cache_service["trajectory_range"] + trajectory_sample = self.cache_service["trajectory_sample"] + print_freq = self.cache_service["print_freq"] + read_trajectory = True traj_file = None traj_step = 1 trajec_file_iterator = None @@ -125,11 +130,15 @@ class CPMDMDParser(MainHierarchicalParser): except ValueError: pass - # Initialize the TRAJECTORY file iterator + # If RANGE is not specified, initialize the TRAJECTORY and FTRAJECTORY + # iterators if files available + ftrajectory_file_iterator = None 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) + if not trajectory_range: + if self.ftrajectory_filepath is not None: + ftrajectory_file_iterator = nomadcore.csvparsing.iread(self.ftrajectory_filepath, columns=range(10), n_conf=n_atoms) + if self.trajectory_filepath is not None: + 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)) @@ -157,29 +166,49 @@ class CPMDMDParser(MainHierarchicalParser): 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(trajec_file_iterator) - except StopIteration: - LOGGER.error("Could not get the next geometries from a TRAJEC file.") - else: - self.backend.addArrayValues("atom_positions", pos, unit="angstrom") - - # 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 print_freq is not None: + if i_frame % print_freq == 0: + + # TRAJEC file + if trajec_file_iterator is not None: + try: + pos = next(trajec_file_iterator) + except StopIteration: + LOGGER.error("Could not get the next geometries from a TRAJEC file.") + else: + self.backend.addArrayValues("atom_positions", pos, unit="angstrom") + + # FTRAJECTORY file + if ftrajectory_file_iterator is not None: + try: + values = next(ftrajectory_file_iterator) + except StopIteration: + LOGGER.error("Could not get the next configuration from a FTRAJECTORY file.") + else: + velocities = values[:, 4:7] + 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") + forces = values[:, 7:10] + self.backend.addArrayValues("atom_forces", forces, unit="forceAu") + + if trajec_file_iterator is None: + pos = values[:, 1:4] + self.backend.addArrayValues("atom_positions", pos, unit="bohr") + + # TRAJECTORY file + if ftrajectory_file_iterator is None: + 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: @@ -204,6 +233,9 @@ class CPMDMDParser(MainHierarchicalParser): self.backend.addRealValue("energy_total", potential_energy, unit="hartree") self.backend.addValue("time_calculation", tcpu) + # Add reference to system + self.backend.addValue("single_configuration_calculation_to_system_ref", sys_id) + # Close sections self.backend.closeSection("section_single_configuration_calculation", scc_id) self.backend.closeSection("section_system", sys_id) diff --git a/test/unittests/cpmd_4.1/geo_opt/xyz/GEOMETRY b/test/unittests/cpmd_4.1/geo_opt/xyz/GEOMETRY new file mode 100644 index 0000000000000000000000000000000000000000..873904884da422dad33e22a6ff59bf43b3309714 --- /dev/null +++ b/test/unittests/cpmd_4.1/geo_opt/xyz/GEOMETRY @@ -0,0 +1,2 @@ + 8.285412756178 7.558904499132 7.558904499132 0.000099666027 0.000000000000 0.000000000000 + 6.832396242085 7.558904499132 7.558904499132 -0.000099666027 0.000000000000 0.000000000000 diff --git a/test/unittests/cpmd_4.1/geo_opt/xyz/GEOMETRY.xyz b/test/unittests/cpmd_4.1/geo_opt/xyz/GEOMETRY.xyz new file mode 100644 index 0000000000000000000000000000000000000000..3d877d082af4882f3cec6a375f74d39a6717fa2a --- /dev/null +++ b/test/unittests/cpmd_4.1/geo_opt/xyz/GEOMETRY.xyz @@ -0,0 +1,4 @@ + 2 +GEOMETRY FILE / created by CPMD + H 4.384451613130 4.000000000000 4.000000000000 0.000052740990 0.000000000000 0.000000000000 + H 3.615548386870 4.000000000000 4.000000000000 -0.000052740990 0.000000000000 0.000000000000 diff --git a/test/unittests/cpmd_4.1/geo_opt/xyz/GEO_OPT.xyz b/test/unittests/cpmd_4.1/geo_opt/xyz/GEO_OPT.xyz new file mode 100644 index 0000000000000000000000000000000000000000..4b1df922939a47d3d0c7a8d8b627a6dad47068bf --- /dev/null +++ b/test/unittests/cpmd_4.1/geo_opt/xyz/GEO_OPT.xyz @@ -0,0 +1,20 @@ + 2 + 1 + H 4.371000000000 4.000000000000 4.000000000000 + H 3.629000000000 4.000000000000 4.000000000000 + 2 + 2 + H 4.386613267056 4.000000000000 4.000000000000 + H 3.613386732944 4.000000000000 4.000000000000 + 2 + 3 + H 4.384560328257 4.000000000000 4.000000000000 + H 3.615439671743 4.000000000000 4.000000000000 + 2 + 4 + H 4.384483260689 4.000000000000 4.000000000000 + H 3.615516739311 4.000000000000 4.000000000000 + 2 + 5 + H 4.384451613130 4.000000000000 4.000000000000 + H 3.615548386870 4.000000000000 4.000000000000 diff --git a/test/unittests/cpmd_4.1/geo_opt/xyz/HESSIAN b/test/unittests/cpmd_4.1/geo_opt/xyz/HESSIAN new file mode 100644 index 0000000000000000000000000000000000000000..87abfb994d499847a053ade25466ab860be519c7 --- /dev/null +++ b/test/unittests/cpmd_4.1/geo_opt/xyz/HESSIAN @@ -0,0 +1,7 @@ + 6 + 0.32162103301424910 2.6424233700674593E-013 3.0211452071429970E-013 -0.32162103301800982 -1.7076247922074472E-013 8.9700778872892222E-014 + 2.6424233700674583E-013 2.1710026863726043E-025 2.4821587770250913E-025 -2.6424233700983574E-013 -1.4029765453914316E-025 7.3697740531939222E-026 + 3.0211452071429965E-013 2.4821587770250913E-025 2.8379109031214153E-025 -3.0211452071783233E-013 -1.6040563044729485E-025 8.4260371788814519E-026 + -0.32162103301800987 -2.6424233700983574E-013 -3.0211452071783233E-013 0.32162103302177036 1.7076247922274146E-013 -8.9700778873941091E-014 + -1.7076247922074470E-013 -1.4029765453914316E-025 -1.6040563044729482E-025 1.7076247922274146E-013 9.0665165882740565E-026 -4.7626012654739061E-026 + 8.9700778872892222E-014 7.3697740531939222E-026 8.4260371788814519E-026 -8.9700778873941104E-014 -4.7626012654739061E-026 2.5017734863276278E-026 diff --git a/test/unittests/cpmd_4.1/geo_opt/xyz/LATEST b/test/unittests/cpmd_4.1/geo_opt/xyz/LATEST new file mode 100644 index 0000000000000000000000000000000000000000..478a14ba44c5fab2e46cd9b5618c667f6728f024 --- /dev/null +++ b/test/unittests/cpmd_4.1/geo_opt/xyz/LATEST @@ -0,0 +1,2 @@ +./RESTART.1 + 6 diff --git a/test/unittests/cpmd_4.1/geo_opt/xyz/RESTART.1 b/test/unittests/cpmd_4.1/geo_opt/xyz/RESTART.1 new file mode 100644 index 0000000000000000000000000000000000000000..a868bd551de4b946f89b84b032d939b07d174c3a Binary files /dev/null and b/test/unittests/cpmd_4.1/geo_opt/xyz/RESTART.1 differ diff --git a/test/unittests/cpmd_4.1/geo_opt/xyz/input.inp b/test/unittests/cpmd_4.1/geo_opt/xyz/input.inp new file mode 100755 index 0000000000000000000000000000000000000000..84ed8c17b20d6c56404ad92b301299ba9c7bafa0 --- /dev/null +++ b/test/unittests/cpmd_4.1/geo_opt/xyz/input.inp @@ -0,0 +1,35 @@ +&INFO +isolated hydrogen molecule. +geometry optimization +&END + +&CPMD + OPTIMIZE GEOMETRY XYZ + CONVERGENCE ORBITALS + 1.0d-7 + CONVERGENCE GEOMETRY + 1.0d-4 +&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 + 4.371 4.000 4.000 + 3.629 4.000 4.000 +&END + diff --git a/test/unittests/cpmd_4.1/geo_opt/xyz/output.out b/test/unittests/cpmd_4.1/geo_opt/xyz/output.out new file mode 100644 index 0000000000000000000000000000000000000000..daa272bd91284bcd0f1c84594bf10314ef23a316 --- /dev/null +++ b/test/unittests/cpmd_4.1/geo_opt/xyz/output.out @@ -0,0 +1,394 @@ + cp_groups: we are using a 1 x 1 grid (groups x nprocs). + PROGRAM CPMD STARTED AT: 2016-07-28 13:15:28.133 + 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/geo_opt/xyz + THE TEMPORARY DIRECTORY IS: + /home/lauri/Dropbox/nomad-dev/nomad-lab-base/parsers/cpmd/test/unittests/cpmd_4.1/geo_opt/xyz + THE PROCESS ID IS: 24054 + THE JOB WAS SUBMITTED BY: lauri + + + ****************************************************************************** + * INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO * + ****************************************************************************** + * isolated hydrogen molecule. * + * geometry optimization * + ****************************************************************************** + + OPTIMIZATION OF IONIC POSITIONS + + USING SEED 123456 TO INIT. PSEUDO RANDOM NUMBER GEN. + PATH TO THE RESTART FILES: ./ + GRAM-SCHMIDT ORTHOGONALIZATION + MAXIMUM NUMBER OF STEPS: 10000 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: 5.0000 + TIME STEP FOR IONS: 5.0000 + CONVERGENCE CRITERIA FOR WAVEFUNCTION OPTIMIZATION: 1.0000E-07 + WAVEFUNCTION OPTIMIZATION BY PRECONDITIONED DIIS + THRESHOLD FOR THE WF-HESSIAN IS 0.5000 + MAXIMUM NUMBER OF VECTORS RETAINED FOR DIIS: 10 + STEPS UNTIL DIIS RESET ON POOR PROGRESS: 10 + FULL ELECTRONIC GRADIENT IS USED + CONVERGENCE CRITERIA FOR GEOMETRY OPTIMIZATION: 1.000000E-04 + GEOMETRY OPTIMIZATION BY GDIIS/BFGS + SIZE OF GDIIS MATRIX: 5 +GEOMETRY OPTIMIZATION IS SAVED ON FILE GEO_OPT.xyz + EMPIRICAL INITIAL HESSIAN (DISCO PARAMETRISATION) + 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 8.259993 7.558904 7.558904 3 + 2 H 6.857816 7.558904 7.558904 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 + + *** GMOPTS| 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 + + ATOM COORDINATES GRADIENTS (-FORCES) + 1 H 8.2600 7.5589 7.5589 0.000E+00 0.000E+00 0.000E+00 + 2 H 6.8578 7.5589 7.5589 0.000E+00 0.000E+00 0.000E+00 + + INITIALIZE EMPIRICAL HESSIAN + <<<<< ASSUMED BONDS >>>>> + 2 <--> 1 + TOTAL NUMBER OF MOLECULAR STRUCTURES: 1 + + ATOM COORDINATES GRADIENTS (-FORCES) + 1 H 8.2600 7.5589 7.5589 0.000E+00 0.000E+00 0.000E+00 + 2 H 6.8578 7.5589 7.5589 0.000E+00 0.000E+00 0.000E+00 + CPU TIME FOR INITIALIZATION 0.88 SECONDS + + + ================================================================ + = GEOMETRY OPTIMIZATION = + ================================================================ + NFI GEMAX CNORM ETOT DETOT TCPU + EWALD| SUM IN REAL SPACE OVER 1* 1* 1 CELLS + 1 3.816E-02 2.886E-03 -1.096898 -1.097E+00 0.24 + 2 8.628E-03 1.041E-03 -1.130803 -3.391E-02 0.23 + 3 2.736E-03 2.293E-04 -1.132376 -1.572E-03 0.23 + 4 6.115E-04 4.235E-05 -1.132456 -8.056E-05 0.25 + 5 1.532E-04 7.007E-06 -1.132459 -3.315E-06 0.23 + 6 3.895E-05 1.396E-06 -1.132460 -1.338E-07 0.24 + 7 6.288E-06 4.459E-07 -1.132460 -7.717E-09 0.24 + 8 7.941E-07 1.282E-07 -1.132460 -4.283E-10 0.24 + 9 1.237E-07 2.861E-08 -1.132460 -1.992E-11 0.25 + 10 2.278E-08 5.401E-09 -1.132460 -8.606E-13 0.26 + + RESTART INFORMATION WRITTEN ON FILE ./RESTART.1 + + ATOM COORDINATES GRADIENTS (-FORCES) + 1 H 8.2600 7.5589 7.5589 -1.780E-02 8.421E-17 7.760E-17 + 2 H 6.8578 7.5589 7.5589 1.780E-02 1.778E-16 1.682E-16 + **************************************************************** + *** TOTAL STEP NR. 10 GEOMETRY STEP NR. 1 *** + *** GNMAX= 1.779860E-02 ETOT= -1.132460 *** + *** GNORM= 1.027603E-02 DETOT= 0.000E+00 *** + *** CNSTR= 0.000000E+00 TCPU= 2.41 *** + **************************************************************** + 1 5.012E-03 9.718E-04 -1.131471 9.887E-04 0.28 + 2 4.287E-04 1.613E-04 -1.132846 -1.375E-03 0.25 + 3 1.489E-04 3.429E-05 -1.132883 -3.658E-05 0.24 + 4 3.265E-05 6.786E-06 -1.132885 -1.887E-06 0.25 + 5 7.649E-06 9.659E-07 -1.132885 -9.037E-08 0.25 + 6 1.707E-06 2.336E-07 -1.132885 -2.124E-09 0.25 + 7 3.870E-07 5.941E-08 -1.132885 -9.984E-11 0.25 + 8 7.619E-08 1.498E-08 -1.132885 -5.241E-12 0.25 + 9 2.806E-08 2.950E-09 -1.132885 -1.432E-13 0.26 + + RESTART INFORMATION WRITTEN ON FILE ./RESTART.1 + + ATOM COORDINATES GRADIENTS (-FORCES) + 1 H 8.2895 7.5589 7.5589 2.695E-03 7.970E-17 7.714E-17 + 2 H 6.8283 7.5589 7.5589 -2.695E-03 1.350E-16 1.183E-16 + **************************************************************** + *** TOTAL STEP NR. 19 GEOMETRY STEP NR. 2 *** + *** GNMAX= 2.694583E-03 [2.95E-02] ETOT= -1.132885 *** + *** GNORM= 1.555718E-03 DETOT= -4.251E-04 *** + *** CNSTR= 0.000000E+00 TCPU= 2.30 *** + **************************************************************** + 1 6.188E-04 1.259E-04 -1.132872 1.251E-05 0.16 + 2 6.604E-05 2.142E-05 -1.132895 -2.326E-05 0.17 + 3 2.121E-05 4.085E-06 -1.132896 -6.178E-07 0.19 + 4 5.282E-06 7.354E-07 -1.132896 -2.729E-08 0.15 + 5 1.316E-06 1.026E-07 -1.132896 -1.177E-09 0.15 + 6 3.022E-07 2.511E-08 -1.132896 -2.822E-11 0.15 + 7 4.514E-08 6.465E-09 -1.132896 -1.464E-12 0.15 + 8 6.481E-09 1.550E-09 -1.132896 -7.150E-14 0.18 + + RESTART INFORMATION WRITTEN ON FILE ./RESTART.1 + + ATOM COORDINATES GRADIENTS (-FORCES) + 1 H 8.2856 7.5589 7.5589 2.320E-04 6.810E-17 9.413E-17 + 2 H 6.8322 7.5589 7.5589 -2.320E-04 1.697E-16 1.268E-16 + **************************************************************** + *** TOTAL STEP NR. 27 GEOMETRY STEP NR. 3 *** + *** GNMAX= 2.319650E-04 [3.88E-03] ETOT= -1.132896 *** + *** GNORM= 1.339250E-04 DETOT= -1.140E-05 *** + *** CNSTR= 0.000000E+00 TCPU= 1.30 *** + **************************************************************** + 1 2.342E-05 4.736E-06 -1.132896 -2.010E-08 0.15 + 2 2.423E-06 8.019E-07 -1.132896 -3.290E-08 0.15 + 3 7.883E-07 1.543E-07 -1.132896 -8.668E-10 0.15 + 4 1.573E-07 2.777E-08 -1.132896 -3.902E-11 0.14 + 5 3.639E-08 3.740E-09 -1.132896 -1.561E-12 0.17 + + RESTART INFORMATION WRITTEN ON FILE ./RESTART.1 + + ATOM COORDINATES GRADIENTS (-FORCES) + 1 H 8.2855 7.5589 7.5589 1.381E-04 1.267E-16 1.019E-16 + 2 H 6.8323 7.5589 7.5589 -1.381E-04 1.620E-16 1.442E-16 + **************************************************************** + *** TOTAL STEP NR. 32 GEOMETRY STEP NR. 4 *** + *** GNMAX= 1.381353E-04 [1.46E-04] ETOT= -1.132896 *** + *** GNORM= 7.975243E-05 DETOT= -5.391E-08 *** + *** CNSTR= 0.000000E+00 TCPU= 0.77 *** + **************************************************************** + 1 9.625E-06 1.945E-06 -1.132896 -8.527E-09 0.16 + 2 9.934E-07 3.289E-07 -1.132896 -5.549E-09 0.17 + 3 3.220E-07 6.333E-08 -1.132896 -1.457E-10 0.19 + 4 7.210E-08 1.115E-08 -1.132896 -6.622E-12 0.17 + 5 1.683E-08 1.567E-09 -1.132896 -4.368E-13 0.16 + + RESTART INFORMATION WRITTEN ON FILE ./RESTART.1 + + TOTAL INTEGRATED ELECTRONIC DENSITY + IN G-SPACE = 2.0000000000 + IN R-SPACE = 2.0000000000 + + (K+E1+L+N+X) TOTAL ENERGY = -1.13289611 A.U. + (K) KINETIC ENERGY = 1.06574787 A.U. + (E1=A-S+R) ELECTROSTATIC ENERGY = -0.49247553 A.U. + (S) ESELF = 0.66490380 A.U. + (R) ESR = 0.15550684 A.U. + (L) LOCAL PSEUDOPOTENTIAL ENERGY = -1.06363345 A.U. + (N) N-L PSEUDOPOTENTIAL ENERGY = 0.00000000 A.U. + (X) EXCHANGE-CORRELATION ENERGY = -0.64253500 A.U. + + + ATOM COORDINATES GRADIENTS (-FORCES) + 1 H 8.2854 7.5589 7.5589 9.967E-05 9.505E-17 6.575E-17 + 2 H 6.8324 7.5589 7.5589 -9.967E-05 1.824E-16 1.335E-16 + **************************************************************** + *** TOTAL STEP NR. 37 GEOMETRY STEP NR. 5 *** + *** GNMAX= 9.966603E-05 [5.98E-05] ETOT= -1.132896 *** + *** GNORM= 5.754221E-05 DETOT= -1.423E-08 *** + *** CNSTR= 0.000000E+00 TCPU= 0.86 *** + **************************************************************** + ================================================================ + = END OF GEOMETRY OPTIMIZATION = + ================================================================ + + + + RESTART INFORMATION WRITTEN ON FILE ./RESTART.1 + + **************************************************************** + * * + * FINAL RESULTS * + * * + **************************************************************** + + ATOM COORDINATES GRADIENTS (-FORCES) + 1 H 8.2854 7.5589 7.5589 9.967E-05 9.505E-17 6.575E-17 + 2 H 6.8324 7.5589 7.5589 -9.967E-05 1.824E-16 1.335E-16 + + **************************************************************** + + + ELECTRONIC GRADIENT: + MAX. COMPONENT = 1.68333E-08 NORM = 1.56737E-09 + NUCLEAR GRADIENT: + MAX. COMPONENT = 9.96660E-05 NORM = 5.75422E-05 + + + TOTAL INTEGRATED ELECTRONIC DENSITY + IN G-SPACE = 2.0000000000 + IN R-SPACE = 2.0000000000 + + (K+E1+L+N+X) TOTAL ENERGY = -1.13289611 A.U. + (K) KINETIC ENERGY = 1.06574787 A.U. + (E1=A-S+R) ELECTROSTATIC ENERGY = -0.49247553 A.U. + (S) ESELF = 0.66490380 A.U. + (R) ESR = 0.15550684 A.U. + (L) LOCAL PSEUDOPOTENTIAL ENERGY = -1.06363345 A.U. + (N) N-L PSEUDOPOTENTIAL ENERGY = 0.00000000 A.U. + (X) EXCHANGE-CORRELATION ENERGY = -0.64253500 A.U. + + **************************************************************** + + + + **************************************************************** + * * + * TIMING * + * * + **************************************************************** + SUBROUTINE CALLS SELF TIME TOTAL TIME + AVERAGE MAXIMUM AVERAGE MAXIMUM + cpmd 1 0.01 0.01 9.03 9.03 + gmopts 1 0.00 0.00 8.52 8.52 + RGMOPT 1 0.00 0.00 8.52 8.52 + updwf 37 0.00 0.00 7.63 7.63 + forcedr 37 0.00 0.00 7.52 7.52 + forces 37 0.00 0.00 7.52 7.52 + forces_a 37 0.00 0.00 5.69 5.69 + rscpot 37 0.00 0.00 5.69 5.69 + vofrho 38 0.00 0.00 4.90 4.90 + INVFFTN 115 3.38 3.38 3.38 3.38 + VOFRHOB 38 0.18 0.18 3.20 3.20 + FWFFTN 77 2.00 2.00 2.00 2.00 + vpsi 39 0.22 0.22 1.95 1.95 + VOFRHOA 38 0.09 0.09 1.71 1.71 + xcener_new 38 0.14 0.14 1.51 1.51 + mikeu 38 1.37 1.37 1.37 1.37 + rhoofr 37 0.26 0.26 1.12 1.12 + 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 + ATRHO 1 0.37 0.37 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 + ppener 38 0.20 0.20 0.20 0.20 + dist_ksmat 1 0.00 0.00 0.13 0.13 + EICALC 38 0.12 0.12 0.12 0.12 + NUMPW 1 0.12 0.12 0.12 0.12 + RINFORCE 1 0.00 0.00 0.11 0.11 + loadpa_b 1 0.11 0.11 0.11 0.11 + FORMFN 1 0.10 0.10 0.10 0.10 + odiis 37 0.10 0.10 0.10 0.10 + loadpa_c 1 0.09 0.09 0.09 0.09 + loadpa_a 1 0.05 0.05 0.05 0.05 + potfor 5 0.04 0.04 0.04 0.04 + forces_b 37 0.01 0.01 0.01 0.01 + **************************************************************** + + CPU TIME : 0 HOURS 0 MINUTES 9.04 SECONDS + ELAPSED TIME : 0 HOURS 0 MINUTES 9.04 SECONDS + *** CPMD| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + + PROGRAM CPMD ENDED AT: 2016-07-28 13:15:37.169 diff --git a/test/unittests/cpmd_4.1/md/ntraj/run.sh b/test/unittests/cpmd_4.1/geo_opt/xyz/run.sh similarity index 100% rename from test/unittests/cpmd_4.1/md/ntraj/run.sh rename to test/unittests/cpmd_4.1/geo_opt/xyz/run.sh diff --git a/test/unittests/cpmd_4.1/md/ftrajectory/ENERGIES b/test/unittests/cpmd_4.1/md/ftrajectory/ENERGIES new file mode 100644 index 0000000000000000000000000000000000000000..0f46ded43b768a12bb7efdc59722e646ac99c4a3 --- /dev/null +++ b/test/unittests/cpmd_4.1/md/ftrajectory/ENERGIES @@ -0,0 +1,5 @@ + 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 0.22 + 4 0.02592222 412.578 -1.1256188624 -1.1236590243 -1.0977368045 0.137607E-03 0.23 + 5 0.02507375 393.180 -1.1245335482 -1.1226658551 -1.0975921059 0.251896E-03 0.23 diff --git a/test/unittests/cpmd_4.1/md/ftrajectory/FTRAJECTORY b/test/unittests/cpmd_4.1/md/ftrajectory/FTRAJECTORY new file mode 100644 index 0000000000000000000000000000000000000000..e8df6b8d3637fdae3cf7be8f449218a9026f79ec --- /dev/null +++ b/test/unittests/cpmd_4.1/md/ftrajectory/FTRAJECTORY @@ -0,0 +1,10 @@ + 1 0.70201340784773 0.00096620207776 0.00104702184853 0.00039772295627 0.00024115257177 0.00026132422738 0.15293653991241 -0.00036559789218 -0.00039617900820 + 1 -0.70201340784773 -0.00096620207776 -0.00104702184853 -0.00039772295627 -0.00024115257177 -0.00026132422738 -0.15293653991238 0.00036559789217 0.00039617900820 + 2 0.70427017594465 0.00192922057414 0.00209059381907 0.00068971096691 0.00024011990909 0.00026020518573 0.11531531366819 -0.00058311803901 -0.00063189402061 + 2 -0.70427017594465 -0.00192922057414 -0.00209059381907 -0.00068971096691 -0.00024011990909 -0.00026020518573 -0.11531531366817 0.00058311803901 0.00063189402061 + 3 0.70753109558303 0.00288716135048 0.00312866333435 0.00088653459833 0.00023876982089 0.00025874216695 0.06550822028645 -0.00065721940559 -0.00071219369650 + 3 -0.70753109558303 -0.00288716135048 -0.00312866333435 -0.00088653459833 -0.00023876982089 -0.00025874216695 -0.06550822028643 0.00065721940559 0.00071219369650 + 4 0.71136245273128 0.00383937914123 0.00416053115468 0.00097170700396 0.00023727594271 0.00025712333073 0.01274038874145 -0.00071521910454 -0.00077504482656 + 4 -0.71136245273128 -0.00383937914123 -0.00416053115468 -0.00097170700396 -0.00023727594271 -0.00025712333073 -0.01274038874143 0.00071521910454 0.00077504482656 + 5 0.71530475161473 0.00478536889215 0.00518564998016 0.00094644268934 0.00023563385430 0.00025534388718 -0.03595092814462 -0.00079338139843 -0.00085974499854 + 5 -0.71530475161473 -0.00478536889215 -0.00518564998016 -0.00094644268934 -0.00023563385430 -0.00025534388718 0.03595092814462 0.00079338139843 0.00085974499854 diff --git a/test/unittests/cpmd_4.1/md/ftrajectory/GEOMETRY b/test/unittests/cpmd_4.1/md/ftrajectory/GEOMETRY new file mode 100644 index 0000000000000000000000000000000000000000..5209a7da40841355f0f4a8ebe66f3f6b212e2da1 --- /dev/null +++ b/test/unittests/cpmd_4.1/md/ftrajectory/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/ftrajectory/GEOMETRY.xyz b/test/unittests/cpmd_4.1/md/ftrajectory/GEOMETRY.xyz new file mode 100644 index 0000000000000000000000000000000000000000..644d2c0c17085461cbc66efb46bfc7ea7b45720e --- /dev/null +++ b/test/unittests/cpmd_4.1/md/ftrajectory/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/ntraj/LATEST b/test/unittests/cpmd_4.1/md/ftrajectory/LATEST similarity index 100% rename from test/unittests/cpmd_4.1/md/ntraj/LATEST rename to test/unittests/cpmd_4.1/md/ftrajectory/LATEST diff --git a/test/unittests/cpmd_4.1/md/ftrajectory/RESTART.1 b/test/unittests/cpmd_4.1/md/ftrajectory/RESTART.1 new file mode 100644 index 0000000000000000000000000000000000000000..6ece95a535a7ff0dcdba46f146e33023d70675f8 Binary files /dev/null and b/test/unittests/cpmd_4.1/md/ftrajectory/RESTART.1 differ diff --git a/test/unittests/cpmd_4.1/md/ntraj/input.inp b/test/unittests/cpmd_4.1/md/ftrajectory/input.inp similarity index 91% rename from test/unittests/cpmd_4.1/md/ntraj/input.inp rename to test/unittests/cpmd_4.1/md/ftrajectory/input.inp index f698db9707b03d92a16eb4bfad7997ac29725e68..13c7d309fb76626671b3aa3ab3ec0fcc0701393c 100755 --- a/test/unittests/cpmd_4.1/md/ntraj/input.inp +++ b/test/unittests/cpmd_4.1/md/ftrajectory/input.inp @@ -6,14 +6,13 @@ simple molecular dynamics deltat=4au &CPMD MOLECULAR DYNAMICS CP - TRAJECTORY XYZ SAMPLE - 7 + TRAJECTORY FORCES TEMPERATURE 50.0D0 MAXSTEP - 50 + 5 TIMESTEP 4.0 &END diff --git a/test/unittests/cpmd_4.1/md/ftrajectory/output.out b/test/unittests/cpmd_4.1/md/ftrajectory/output.out new file mode 100644 index 0000000000000000000000000000000000000000..fe4c66ac9ea533be82331cb0115abf3948a1493f --- /dev/null +++ b/test/unittests/cpmd_4.1/md/ftrajectory/output.out @@ -0,0 +1,328 @@ + cp_groups: we are using a 1 x 1 grid (groups x nprocs). + PROGRAM CPMD STARTED AT: 2016-07-28 10:04:03.110 + 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/ftrajectory + THE TEMPORARY DIRECTORY IS: + /home/lauri/Dropbox/nomad-dev/nomad-lab-base/parsers/cpmd/test/unittests/cpmd_4.1/md/ftrajectory + THE PROCESS ID IS: 13279 + 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: 0.47 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: 1.03 SECONDS + + **************************************************************** + * ATOMIC COORDINATES * + **************************************************************** + 1 H 0.702013 0.000966 0.001047 + 2 H -0.702013 -0.000966 -0.001047 + **************************************************************** + + + TOTAL INTEGRATED ELECTRONIC DENSITY + IN G-SPACE = 2.0000000000 + IN R-SPACE = 2.0000000000 + + (K+E1+L+N+X) TOTAL ENERGY = -1.10234921 A.U. + (K) KINETIC ENERGY = 0.83136071 A.U. + (E1=A-S+R) ELECTROSTATIC ENERGY = -0.48680398 A.U. + (S) ESELF = 0.66490380 A.U. + (R) ESR = 0.17235462 A.U. + (L) LOCAL PSEUDOPOTENTIAL ENERGY = -0.86930120 A.U. + (N) N-L PSEUDOPOTENTIAL ENERGY = 0.00000000 A.U. + (X) EXCHANGE-CORRELATION ENERGY = -0.57760473 A.U. + + NFI EKINC TEMPP EKS ECLASSIC EHAM DIS TCPU + 1 0.00473 110.1 -1.10235 -1.10183 -1.09710 0.289E-05 0.24 + 2 0.01424 232.5 -1.11287 -1.11176 -1.09752 0.182E-04 0.24 + 3 0.02229 352.0 -1.12169 -1.12002 -1.09773 0.596E-04 0.22 + 4 0.02592 412.6 -1.12562 -1.12366 -1.09774 0.138E-03 0.23 + 5 0.02507 393.2 -1.12453 -1.12267 -1.09759 0.252E-03 0.23 + + 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 0.2318 + + **************************************************************** + * * + * 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 0.00 0.00 2.66 2.66 + mdpt 1 0.00 0.00 2.19 2.19 + mdmain 1 0.00 0.00 2.19 2.19 + forcedr 6 0.00 0.00 1.38 1.38 + forces 6 0.00 0.00 1.38 1.38 + vofrho 7 0.00 0.00 1.22 1.22 + forces_a 6 0.00 0.00 1.10 1.10 + rscpot 6 0.00 0.00 1.10 1.10 + VOFRHOB 7 0.03 0.03 0.83 0.83 + initrun 1 0.00 0.00 0.80 0.80 + rinitwf 1 0.00 0.00 0.80 0.80 + ATOMWF 1 0.00 0.00 0.80 0.80 + INVFFTN 22 0.71 0.71 0.71 0.71 + xcener_new 7 0.03 0.03 0.47 0.47 + mikeu 7 0.45 0.45 0.45 0.45 + FWFFTN 15 0.41 0.41 0.41 0.41 + ATRHO 1 0.35 0.35 0.39 0.39 + vpsi 8 0.03 0.03 0.39 0.39 + VOFRHOA 7 0.01 0.01 0.39 0.39 + rinit 1 0.00 0.00 0.25 0.25 + rggen 1 0.01 0.01 0.25 0.25 + 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 + loadpa_b 1 0.10 0.10 0.10 0.10 + loadpa_c 1 0.09 0.09 0.09 0.09 + FORMFN 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 + ovlap 17 0.00 0.00 0.00 0.00 + PHFAC 6 0.00 0.00 0.00 0.00 + ovlap_grps_a 17 0.00 0.00 0.00 0.00 + **************************************************************** + + CPU TIME : 0 HOURS 0 MINUTES 2.66 SECONDS + ELAPSED TIME : 0 HOURS 0 MINUTES 2.67 SECONDS + *** CPMD| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + + PROGRAM CPMD ENDED AT: 2016-07-28 10:04:05.773 diff --git a/test/unittests/cpmd_4.1/md/ftrajectory/run.sh b/test/unittests/cpmd_4.1/md/ftrajectory/run.sh new file mode 100755 index 0000000000000000000000000000000000000000..74ce0ca5a55a21a25741d586bcf4cb42c8f14590 --- /dev/null +++ b/test/unittests/cpmd_4.1/md/ftrajectory/run.sh @@ -0,0 +1,3 @@ +export CPMD_PP_LIBRARY_PATH=../../ +export OMP_NUM_THREADS=1 +cpmd41 input.inp > output.out diff --git a/test/unittests/cpmd_4.1/md/ntraj/ENERGIES b/test/unittests/cpmd_4.1/md/ntraj/ENERGIES deleted file mode 100644 index 02c7d2ffbe3c10b2428d26bd946366d011c75922..0000000000000000000000000000000000000000 --- a/test/unittests/cpmd_4.1/md/ntraj/ENERGIES +++ /dev/null @@ -1,50 +0,0 @@ - 1 0.00472945 110.096 -1.1023492072 -1.1018262261 -1.0970967730 0.288545E-05 0.25 - 2 0.01424065 232.496 -1.1128688938 -1.1117644858 -1.0975238350 0.182162E-04 0.26 - 3 0.02228702 351.956 -1.1216882365 -1.1200163669 -1.0977293448 0.596327E-04 0.25 - 4 0.02592222 412.578 -1.1256188624 -1.1236590243 -1.0977368045 0.137607E-03 0.25 - 5 0.02507375 393.180 -1.1245335482 -1.1226658551 -1.0975921059 0.251896E-03 0.41 - 6 0.02170348 311.439 -1.1206087528 -1.1191293469 -1.0974258636 0.389716E-03 0.35 - 7 0.01806912 208.928 -1.1163887071 -1.1153962539 -1.0973271357 0.530786E-03 0.36 - 8 0.01550309 123.508 -1.1133979574 -1.1128112667 -1.0973081718 0.656212E-03 0.37 - 9 0.01428927 71.351 -1.1119610076 -1.1116220739 -1.0973328023 0.755177E-03 0.37 - 10 0.01412005 48.653 -1.1117171754 -1.1114860650 -1.0973660187 0.826435E-03 0.39 - 11 0.01454963 43.205 -1.1121477411 -1.1119425095 -1.0973928823 0.875667E-03 0.33 - 12 0.01522198 44.147 -1.1128400647 -1.1126303571 -1.0974083755 0.911456E-03 0.26 - 13 0.01592316 45.526 -1.1135548344 -1.1133385763 -1.0974154187 0.942258E-03 0.24 - 14 0.01655033 45.568 -1.1141854503 -1.1139689917 -1.0974186637 0.974901E-03 0.24 - 15 0.01706605 44.715 -1.1146975180 -1.1144851121 -1.0974190627 0.101412E-02 0.24 - 16 0.01746680 44.005 -1.1150947618 -1.1148857283 -1.0974189329 0.106282E-02 0.26 - 17 0.01776074 44.244 -1.1153899632 -1.1151797929 -1.0974190575 0.112264E-02 0.35 - 18 0.01795742 45.772 -1.1155935307 -1.1153761050 -1.0974186815 0.119434E-02 0.35 - 19 0.01806576 48.537 -1.1157147808 -1.1154842182 -1.0974184559 0.127815E-02 0.34 - 20 0.01809373 52.255 -1.1157599169 -1.1155116921 -1.0974179583 0.137401E-02 0.32 - 21 0.01805054 56.516 -1.1157360008 -1.1154675379 -1.0974169961 0.148167E-02 0.23 - 22 0.01794636 60.905 -1.1156512292 -1.1153619159 -1.0974155607 0.160074E-02 0.23 - 23 0.01779314 65.074 -1.1155167676 -1.1152076534 -1.0974145094 0.173073E-02 0.23 - 24 0.01760410 68.722 -1.1153426839 -1.1150162383 -1.0974121397 0.187108E-02 0.23 - 25 0.01739640 71.638 -1.1151469827 -1.1148066858 -1.0974102809 0.202107E-02 0.23 - 26 0.01718921 73.709 -1.1149481806 -1.1145980447 -1.0974088338 0.217994E-02 0.23 - 27 0.01699582 74.870 -1.1147573603 -1.1144017101 -1.0974058862 0.234681E-02 0.23 - 28 0.01683495 75.111 -1.1145981234 -1.1142413309 -1.0974063855 0.252070E-02 0.23 - 29 0.01670265 74.489 -1.1144603569 -1.1141065157 -1.0974038654 0.270054E-02 0.22 - 30 0.01661442 73.081 -1.1143644220 -1.1140172732 -1.0974028537 0.288524E-02 0.23 - 31 0.01655815 70.980 -1.1143033888 -1.1139662190 -1.0974080684 0.307358E-02 0.24 - 32 0.01650569 68.325 -1.1142240908 -1.1138995296 -1.0973938363 0.326432E-02 0.22 - 33 0.01657766 65.255 -1.1142857160 -1.1139757411 -1.0973980782 0.345624E-02 0.23 - 34 0.01674936 61.905 -1.1144438592 -1.1141497957 -1.0974004352 0.364807E-02 0.23 - 35 0.01702316 58.440 -1.1146791594 -1.1144015566 -1.0973784004 0.383857E-02 0.22 - 36 0.01763441 55.015 -1.1152782856 -1.1150169543 -1.0973825424 0.402661E-02 0.23 - 37 0.01848514 51.771 -1.1161573098 -1.1159113844 -1.0974262399 0.421112E-02 0.22 - 38 0.01897016 48.857 -1.1166648547 -1.1164327728 -1.0974626172 0.439118E-02 0.22 - 39 0.01858750 46.386 -1.1162605862 -1.1160402423 -1.0974527395 0.456614E-02 0.24 - 40 0.01744917 44.419 -1.1150750202 -1.1148640199 -1.0974148488 0.473558E-02 0.23 - 41 0.01610603 42.978 -1.1136853843 -1.1134812305 -1.0973752036 0.489928E-02 0.23 - 42 0.01516204 42.048 -1.1127114865 -1.1125117498 -1.0973497053 0.505718E-02 0.22 - 43 0.01497724 41.607 -1.1125324644 -1.1123348215 -1.0973575818 0.520925E-02 0.23 - 44 0.01549914 41.655 -1.1130663421 -1.1128684718 -1.0973693342 0.535541E-02 0.23 - 45 0.01649282 42.196 -1.1140950557 -1.1138946136 -1.0974017920 0.549556E-02 0.22 - 46 0.01752242 43.235 -1.1151502868 -1.1149449129 -1.0974224937 0.562968E-02 0.22 - 47 0.01826876 44.768 -1.1159079382 -1.1156952780 -1.0974265218 0.575782E-02 0.23 - 48 0.01863973 46.745 -1.1162911025 -1.1160690555 -1.0974293221 0.588031E-02 0.23 - 49 0.01862430 49.045 -1.1162747263 -1.1160417513 -1.0974174556 0.599772E-02 0.23 - 50 0.01840782 51.542 -1.1160488582 -1.1158040226 -1.0973962069 0.611084E-02 0.22 diff --git a/test/unittests/cpmd_4.1/md/ntraj/GEOMETRY b/test/unittests/cpmd_4.1/md/ntraj/GEOMETRY deleted file mode 100644 index 99afcdea42b2a843f164962a4b29f8f63c16e0db..0000000000000000000000000000000000000000 --- a/test/unittests/cpmd_4.1/md/ntraj/GEOMETRY +++ /dev/null @@ -1,2 +0,0 @@ - 0.740084462274 0.045946600273 0.049790097126 -0.000187193069 0.000212525459 0.000230307582 - -0.740084462274 -0.045946600273 -0.049790097126 0.000187193069 -0.000212525459 -0.000230307582 diff --git a/test/unittests/cpmd_4.1/md/ntraj/GEOMETRY.xyz b/test/unittests/cpmd_4.1/md/ntraj/GEOMETRY.xyz deleted file mode 100644 index 15b6e3715df41db74f68e973a4f400d438925ea8..0000000000000000000000000000000000000000 --- a/test/unittests/cpmd_4.1/md/ntraj/GEOMETRY.xyz +++ /dev/null @@ -1,4 +0,0 @@ - 2 -GEOMETRY FILE / created by CPMD - H 0.391635831546 0.024313893781 0.026347784726 -0.000099058306 0.000112463630 0.000121873524 - H -0.391635831546 -0.024313893781 -0.026347784726 0.000099058306 -0.000112463630 -0.000121873524 diff --git a/test/unittests/cpmd_4.1/md/ntraj/RESTART.1 b/test/unittests/cpmd_4.1/md/ntraj/RESTART.1 deleted file mode 100644 index f5d79f1aa4969bb60dbcfbca85786c92e0135968..0000000000000000000000000000000000000000 Binary files a/test/unittests/cpmd_4.1/md/ntraj/RESTART.1 and /dev/null differ diff --git a/test/unittests/cpmd_4.1/md/ntraj/TRAJEC.xyz b/test/unittests/cpmd_4.1/md/ntraj/TRAJEC.xyz deleted file mode 100644 index d7e893edac3a468b0365fd495885b9e580dc4101..0000000000000000000000000000000000000000 --- a/test/unittests/cpmd_4.1/md/ntraj/TRAJEC.xyz +++ /dev/null @@ -1,32 +0,0 @@ - 2 - STEP: 1 - H 0.371489 0.000511 0.000554 - H -0.371489 -0.000511 -0.000554 - 2 - STEP: 8 - H 0.383197 0.004012 0.004347 - H -0.383197 -0.004012 -0.004347 - 2 - STEP: 15 - H 0.383871 0.007377 0.007994 - H -0.383871 -0.007377 -0.007994 - 2 - STEP: 22 - H 0.384963 0.010793 0.011696 - H -0.384963 -0.010793 -0.011696 - 2 - STEP: 29 - H 0.388694 0.014276 0.015471 - H -0.388694 -0.014276 -0.015471 - 2 - STEP: 36 - H 0.392062 0.017736 0.019220 - H -0.392062 -0.017736 -0.019220 - 2 - STEP: 43 - H 0.393167 0.021093 0.022857 - H -0.393167 -0.021093 -0.022857 - 2 - STEP: 50 - H 0.391636 0.024314 0.026348 - H -0.391636 -0.024314 -0.026348 diff --git a/test/unittests/cpmd_4.1/md/ntraj/TRAJECTORY b/test/unittests/cpmd_4.1/md/ntraj/TRAJECTORY deleted file mode 100644 index 147fc65673d4ce8634102b0975449d3d083d49b7..0000000000000000000000000000000000000000 --- a/test/unittests/cpmd_4.1/md/ntraj/TRAJECTORY +++ /dev/null @@ -1,16 +0,0 @@ - 1 0.70201340784773 0.00096620207776 0.00104702184853 0.00039772295627 0.00024115257177 0.00026132422738 - 1 -0.70201340784773 -0.00096620207776 -0.00104702184853 -0.00039772295627 -0.00024115257177 -0.00026132422738 - 8 0.72413746922406 0.00758077571951 0.00821488383936 0.00045168695311 0.00023026062676 0.00024952121008 - 8 -0.72413746922405 -0.00758077571951 -0.00821488383936 -0.00045168695311 -0.00023026062676 -0.00024952121008 - 15 0.72541141597952 0.01393987125682 0.01510589837261 -0.00005721545799 0.00022729120928 0.00024630345710 - 15 -0.72541141597952 -0.01393987125682 -0.01510589837261 0.00005721545799 -0.00022729120928 -0.00024630345710 - 22 0.72747394256230 0.02039650999872 0.02210261801843 0.00019672664260 0.00023370463452 0.00025325351120 - 22 -0.72747394256230 -0.02039650999872 -0.02210261801843 -0.00019672664260 -0.00023370463452 -0.00025325351120 - 29 0.73452501168355 0.02697851051064 0.02923519332609 0.00026869648870 0.00023529533309 0.00025497768132 - 29 -0.73452501168355 -0.02697851051064 -0.02923519332609 -0.00026869648870 -0.00023529533309 -0.00025497768132 - 36 0.74089002841595 0.03351605907910 0.03631961522256 0.00016284624701 0.00023068680238 0.00024998447545 - 36 -0.74089002841595 -0.03351605907910 -0.03631961522256 -0.00016284624701 -0.00023068680238 -0.00024998447545 - 43 0.74297731733313 0.03986003838995 0.04319430656967 -0.00001474968690 0.00022219565239 0.00024078445181 - 43 -0.74297731733313 -0.03986003838995 -0.04319430656967 0.00001474968690 -0.00022219565239 -0.00024078445181 - 50 0.74008446227396 0.04594660027294 0.04979009712617 -0.00018719306900 0.00021252545941 0.00023030758250 - 50 -0.74008446227396 -0.04594660027294 -0.04979009712617 0.00018719306900 -0.00021252545941 -0.00023030758250 diff --git a/test/unittests/cpmd_4.1/md/nve/ENERGIES b/test/unittests/cpmd_4.1/md/nve/ENERGIES index 2e1b5cffe89fecba53fe53e3f5050b70cdfd1703..37844a9fded270c172da7b3feb2c1f8e38ea8db4 100644 --- a/test/unittests/cpmd_4.1/md/nve/ENERGIES +++ b/test/unittests/cpmd_4.1/md/nve/ENERGIES @@ -1,5 +1,5 @@ 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 + 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 0.28 + 5 0.02507375 393.180 -1.1245335482 -1.1226658551 -1.0975921059 0.251896E-03 0.28 diff --git a/test/unittests/cpmd_4.1/md/nve/FTRAJECTORY b/test/unittests/cpmd_4.1/md/nve/FTRAJECTORY new file mode 100644 index 0000000000000000000000000000000000000000..e8df6b8d3637fdae3cf7be8f449218a9026f79ec --- /dev/null +++ b/test/unittests/cpmd_4.1/md/nve/FTRAJECTORY @@ -0,0 +1,10 @@ + 1 0.70201340784773 0.00096620207776 0.00104702184853 0.00039772295627 0.00024115257177 0.00026132422738 0.15293653991241 -0.00036559789218 -0.00039617900820 + 1 -0.70201340784773 -0.00096620207776 -0.00104702184853 -0.00039772295627 -0.00024115257177 -0.00026132422738 -0.15293653991238 0.00036559789217 0.00039617900820 + 2 0.70427017594465 0.00192922057414 0.00209059381907 0.00068971096691 0.00024011990909 0.00026020518573 0.11531531366819 -0.00058311803901 -0.00063189402061 + 2 -0.70427017594465 -0.00192922057414 -0.00209059381907 -0.00068971096691 -0.00024011990909 -0.00026020518573 -0.11531531366817 0.00058311803901 0.00063189402061 + 3 0.70753109558303 0.00288716135048 0.00312866333435 0.00088653459833 0.00023876982089 0.00025874216695 0.06550822028645 -0.00065721940559 -0.00071219369650 + 3 -0.70753109558303 -0.00288716135048 -0.00312866333435 -0.00088653459833 -0.00023876982089 -0.00025874216695 -0.06550822028643 0.00065721940559 0.00071219369650 + 4 0.71136245273128 0.00383937914123 0.00416053115468 0.00097170700396 0.00023727594271 0.00025712333073 0.01274038874145 -0.00071521910454 -0.00077504482656 + 4 -0.71136245273128 -0.00383937914123 -0.00416053115468 -0.00097170700396 -0.00023727594271 -0.00025712333073 -0.01274038874143 0.00071521910454 0.00077504482656 + 5 0.71530475161473 0.00478536889215 0.00518564998016 0.00094644268934 0.00023563385430 0.00025534388718 -0.03595092814462 -0.00079338139843 -0.00085974499854 + 5 -0.71530475161473 -0.00478536889215 -0.00518564998016 -0.00094644268934 -0.00023563385430 -0.00025534388718 0.03595092814462 0.00079338139843 0.00085974499854 diff --git a/test/unittests/cpmd_4.1/md/nve/RESTART.1 b/test/unittests/cpmd_4.1/md/nve/RESTART.1 index 7ce3c028478c60d90cc0e4a4374c823cbc0526dd..1e6fd36998ab71dc70652463360852ea8296ac7d 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/input.inp b/test/unittests/cpmd_4.1/md/nve/input.inp index c442d2456ff62e83804949876a299079f47c9296..53dfb6d6d960cc668c0cf14d87ac64feeae52ea4 100755 --- a/test/unittests/cpmd_4.1/md/nve/input.inp +++ b/test/unittests/cpmd_4.1/md/nve/input.inp @@ -6,7 +6,7 @@ simple molecular dynamics deltat=4au &CPMD MOLECULAR DYNAMICS CP - TRAJECTORY XYZ + TRAJECTORY XYZ FORCES TEMPERATURE 50.0D0 diff --git a/test/unittests/cpmd_4.1/md/nve/output.out b/test/unittests/cpmd_4.1/md/nve/output.out index dfd0bcc71d224df87dfabed431b4081142b4d450..b9b0e6fdcbc7cdef736b73282408c859eeab414a 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: 2016-07-27 13:27:37.467 + PROGRAM CPMD STARTED AT: 2016-07-28 11:09:25.169 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: 9982 + THE PROCESS ID IS: 16100 THE JOB WAS SUBMITTED BY: lauri @@ -154,7 +154,7 @@ 1S ALPHA= 1.0000 OCCUPATION= 1.00 - INITIALIZATION TIME: 0.49 SECONDS + INITIALIZATION TIME: 0.48 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: 1.09 SECONDS + TIME FOR INITIALIZATION: 1.06 SECONDS **************************************************************** * ATOMIC COORDINATES * @@ -214,10 +214,10 @@ NFI EKINC TEMPP EKS ECLASSIC EHAM DIS TCPU 1 0.00473 110.1 -1.10235 -1.10183 -1.09710 0.289E-05 0.24 - 2 0.01424 232.5 -1.11287 -1.11176 -1.09752 0.182E-04 0.24 - 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 + 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 0.28 + 5 0.02507 393.2 -1.12453 -1.12267 -1.09759 0.252E-03 0.28 RESTART INFORMATION WRITTEN ON FILE ./RESTART.1 @@ -236,7 +236,7 @@ CONSTRAINTS ENERGY 0.000000 0.00000 RESTRAINTS ENERGY 0.000000 0.00000 ION DISPLACEMENT 0.940474E-04 0.917156E-04 - CPU TIME 0.2370 + CPU TIME 0.2596 **************************************************************** * * @@ -282,47 +282,45 @@ **************************************************************** SUBROUTINE CALLS SELF TIME TOTAL TIME AVERAGE MAXIMUM AVERAGE MAXIMUM - 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 + cpmd 1 0.00 0.00 2.84 2.84 + 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 1.53 1.53 + forces 6 0.00 0.00 1.53 1.53 + vofrho 7 0.00 0.00 1.33 1.33 + 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 0.91 0.91 + 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 + INVFFTN 22 0.77 0.77 0.77 0.77 + xcener_new 7 0.04 0.04 0.52 0.52 + mikeu 7 0.48 0.48 0.48 0.48 + FWFFTN 15 0.44 0.44 0.44 0.44 + VOFRHOA 7 0.02 0.02 0.43 0.43 + vpsi 8 0.04 0.04 0.42 0.42 + ATRHO 1 0.36 0.36 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 0.25 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 + loadpa 1 0.01 0.01 0.26 0.26 + rhoofr 6 0.04 0.04 0.20 0.20 + RINFORCE 1 0.00 0.00 0.11 0.11 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_c 1 0.09 0.09 0.09 0.09 + dist_ksmat 1 0.00 0.00 0.10 0.10 + NUMPW 1 0.10 0.10 0.10 0.10 potfor 6 0.06 0.06 0.06 0.06 + ppener 7 0.05 0.05 0.05 0.05 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 + fftprp 1 0.01 0.01 0.01 0.01 **************************************************************** - CPU TIME : 0 HOURS 0 MINUTES 2.75 SECONDS - ELAPSED TIME : 0 HOURS 0 MINUTES 2.77 SECONDS + CPU TIME : 0 HOURS 0 MINUTES 2.84 SECONDS + ELAPSED TIME : 0 HOURS 0 MINUTES 2.84 SECONDS *** CPMD| SIZE OF THE PROGRAM IS NOT AVAILABLE *** - PROGRAM CPMD ENDED AT: 2016-07-27 13:27:40.229 + PROGRAM CPMD ENDED AT: 2016-07-28 11:09:28.012 diff --git a/test/unittests/cpmd_4.1/md/range/ENERGIES b/test/unittests/cpmd_4.1/md/range/ENERGIES index 66527e259ee4971fda2affb0f5b88d45f9305c62..46d3b0ded94e27d2292acbc7ff065c05d675e3c8 100644 --- a/test/unittests/cpmd_4.1/md/range/ENERGIES +++ b/test/unittests/cpmd_4.1/md/range/ENERGIES @@ -1,50 +1,5 @@ - 1 0.00472945 110.096 -1.1023492072 -1.1018262261 -1.0970967730 0.288545E-05 0.24 - 2 0.01424065 232.496 -1.1128688938 -1.1117644858 -1.0975238350 0.182162E-04 0.26 - 3 0.02228702 351.956 -1.1216882365 -1.1200163669 -1.0977293448 0.596327E-04 0.24 + 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 0.23 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 0.23 - 7 0.01806912 208.928 -1.1163887071 -1.1153962539 -1.0973271357 0.530786E-03 0.23 - 8 0.01550309 123.508 -1.1133979574 -1.1128112667 -1.0973081718 0.656212E-03 0.22 - 9 0.01428927 71.351 -1.1119610076 -1.1116220739 -1.0973328023 0.755177E-03 0.24 - 10 0.01412005 48.653 -1.1117171754 -1.1114860650 -1.0973660187 0.826435E-03 0.23 - 11 0.01454963 43.205 -1.1121477411 -1.1119425095 -1.0973928823 0.875667E-03 0.23 - 12 0.01522198 44.147 -1.1128400647 -1.1126303571 -1.0974083755 0.911456E-03 0.23 - 13 0.01592316 45.526 -1.1135548344 -1.1133385763 -1.0974154187 0.942258E-03 0.26 - 14 0.01655033 45.568 -1.1141854503 -1.1139689917 -1.0974186637 0.974901E-03 0.31 - 15 0.01706605 44.715 -1.1146975180 -1.1144851121 -1.0974190627 0.101412E-02 0.32 - 16 0.01746680 44.005 -1.1150947618 -1.1148857283 -1.0974189329 0.106282E-02 0.31 - 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 0.24 - 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 0.30 - 22 0.01794636 60.905 -1.1156512292 -1.1153619159 -1.0974155607 0.160074E-02 0.30 - 23 0.01779314 65.074 -1.1155167676 -1.1152076534 -1.0974145094 0.173073E-02 0.31 - 24 0.01760410 68.722 -1.1153426839 -1.1150162383 -1.0974121397 0.187108E-02 0.28 - 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 0.24 - 28 0.01683495 75.111 -1.1145981234 -1.1142413309 -1.0974063855 0.252070E-02 0.24 - 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 0.22 - 34 0.01674936 61.905 -1.1144438592 -1.1141497957 -1.0974004352 0.364807E-02 0.23 - 35 0.01702316 58.440 -1.1146791594 -1.1144015566 -1.0973784004 0.383857E-02 0.22 - 36 0.01763441 55.015 -1.1152782856 -1.1150169543 -1.0973825424 0.402661E-02 0.22 - 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 0.23 - 45 0.01649282 42.196 -1.1140950557 -1.1138946136 -1.0974017920 0.549556E-02 0.23 - 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 0.24 - 48 0.01863973 46.745 -1.1162911025 -1.1160690555 -1.0974293221 0.588031E-02 0.24 - 49 0.01862430 49.045 -1.1162747263 -1.1160417513 -1.0974174556 0.599772E-02 0.23 - 50 0.01840782 51.542 -1.1160488582 -1.1158040226 -1.0973962069 0.611084E-02 0.23 diff --git a/test/unittests/cpmd_4.1/md/range/GEOMETRY b/test/unittests/cpmd_4.1/md/range/GEOMETRY index 99afcdea42b2a843f164962a4b29f8f63c16e0db..5209a7da40841355f0f4a8ebe66f3f6b212e2da1 100644 --- a/test/unittests/cpmd_4.1/md/range/GEOMETRY +++ b/test/unittests/cpmd_4.1/md/range/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/range/GEOMETRY.xyz b/test/unittests/cpmd_4.1/md/range/GEOMETRY.xyz index 15b6e3715df41db74f68e973a4f400d438925ea8..644d2c0c17085461cbc66efb46bfc7ea7b45720e 100644 --- a/test/unittests/cpmd_4.1/md/range/GEOMETRY.xyz +++ b/test/unittests/cpmd_4.1/md/range/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/range/RESTART.1 b/test/unittests/cpmd_4.1/md/range/RESTART.1 index 2936a0715180dfde3899160f87fd3d7b863c6d64..141ed8984699c1e05eeba669c74787a68baef261 100644 Binary files a/test/unittests/cpmd_4.1/md/range/RESTART.1 and b/test/unittests/cpmd_4.1/md/range/RESTART.1 differ diff --git a/test/unittests/cpmd_4.1/md/range/TRAJEC.xyz b/test/unittests/cpmd_4.1/md/range/TRAJEC.xyz index a550acbe47e5c4d4cdbabaf65041ca6e70a0fa95..fee8c8bf77f773de37d0a9814c1e80b2ac365089 100644 --- a/test/unittests/cpmd_4.1/md/range/TRAJEC.xyz +++ b/test/unittests/cpmd_4.1/md/range/TRAJEC.xyz @@ -18,183 +18,3 @@ STEP: 5 H 0.378523 0.002532 0.002744 H -0.378523 -0.002532 -0.002744 - 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2 - STEP: 44 - H 0.393109 0.021562 0.023366 - H -0.393109 -0.021562 -0.023366 - 2 - STEP: 45 - H 0.392997 0.022028 0.023871 - H -0.392997 -0.022028 -0.023871 - 2 - STEP: 46 - H 0.392831 0.022491 0.024373 - H -0.392831 -0.022491 -0.024373 - 2 - STEP: 47 - H 0.392610 0.022951 0.024871 - H -0.392610 -0.022951 -0.024871 - 2 - STEP: 48 - H 0.392336 0.023409 0.025367 - H -0.392336 -0.023409 -0.025367 - 2 - STEP: 49 - H 0.392010 0.023863 0.025859 - H -0.392010 -0.023863 -0.025859 - 2 - STEP: 50 - H 0.391636 0.024314 0.026348 - H -0.391636 -0.024314 -0.026348 diff --git a/test/unittests/cpmd_4.1/md/range/TRAJECTORY b/test/unittests/cpmd_4.1/md/range/TRAJECTORY index 4a0b27c83a61ed24297d986a6125b78fa403fbf7..e9ab587e1ca93208821f58da582e5e649586391b 100644 --- a/test/unittests/cpmd_4.1/md/range/TRAJECTORY +++ b/test/unittests/cpmd_4.1/md/range/TRAJECTORY @@ -3,48 +3,3 @@ 3 0.70753109558303 0.00288716135048 0.00312866333435 0.00088653459833 0.00023876982089 0.00025874216695 4 0.71136245273128 0.00383937914123 0.00416053115468 0.00097170700396 0.00023727594271 0.00025712333073 5 0.71530475161473 0.00478536889215 0.00518564998016 0.00094644268934 0.00023563385430 0.00025534388718 - 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46 0.74234263971264 0.04250238552716 0.04605771617754 -0.00009134238039 0.00021810231001 0.00023634953748 - 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 - 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 diff --git a/test/unittests/cpmd_4.1/md/range/input.inp b/test/unittests/cpmd_4.1/md/range/input.inp index fe4ecddad9c5b2f9a6fbb209929cb23ef1e501df..2f972b7a6ed6f46acd57a924a57c7ee7b01b8e54 100755 --- a/test/unittests/cpmd_4.1/md/range/input.inp +++ b/test/unittests/cpmd_4.1/md/range/input.inp @@ -13,7 +13,7 @@ simple molecular dynamics deltat=4au 50.0D0 MAXSTEP - 50 + 5 TIMESTEP 4.0 &END diff --git a/test/unittests/cpmd_4.1/md/range/output.out b/test/unittests/cpmd_4.1/md/range/output.out index d9f7f17e29a6c20ac1e9ab1f1af97fca1b4930c8..b7055875562d40e47d6a137fe993d5c4ee0ac30b 100644 --- a/test/unittests/cpmd_4.1/md/range/output.out +++ b/test/unittests/cpmd_4.1/md/range/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 14:28:14.740 + PROGRAM CPMD STARTED AT: 2016-07-28 11:16:10.699 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/range THE TEMPORARY DIRECTORY IS: /home/lauri/Dropbox/nomad-dev/nomad-lab-base/parsers/cpmd/test/unittests/cpmd_4.1/md/range - THE PROCESS ID IS: 11976 + THE PROCESS ID IS: 16807 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: 0.50 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: 1.06 SECONDS + TIME FOR INITIALIZATION: 1.08 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 0.24 - 2 0.01424 232.5 -1.11287 -1.11176 -1.09752 0.182E-04 0.26 - 3 0.02229 352.0 -1.12169 -1.12002 -1.09773 0.596E-04 0.24 + 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 0.23 4 0.02592 412.6 -1.12562 -1.12366 -1.09774 0.138E-03 0.24 5 0.02507 393.2 -1.12453 -1.12267 -1.09759 0.252E-03 0.23 - 6 0.02170 311.4 -1.12061 -1.11913 -1.09743 0.390E-03 0.23 - 7 0.01807 208.9 -1.11639 -1.11540 -1.09733 0.531E-03 0.23 - 8 0.01550 123.5 -1.11340 -1.11281 -1.09731 0.656E-03 0.22 - 9 0.01429 71.4 -1.11196 -1.11162 -1.09733 0.755E-03 0.24 - 10 0.01412 48.7 -1.11172 -1.11149 -1.09737 0.826E-03 0.23 - 11 0.01455 43.2 -1.11215 -1.11194 -1.09739 0.876E-03 0.23 - 12 0.01522 44.1 -1.11284 -1.11263 -1.09741 0.911E-03 0.23 - 13 0.01592 45.5 -1.11355 -1.11334 -1.09742 0.942E-03 0.26 - 14 0.01655 45.6 -1.11419 -1.11397 -1.09742 0.975E-03 0.31 - 15 0.01707 44.7 -1.11470 -1.11449 -1.09742 0.101E-02 0.32 - 16 0.01747 44.0 -1.11509 -1.11489 -1.09742 0.106E-02 0.31 - 17 0.01776 44.2 -1.11539 -1.11518 -1.09742 0.112E-02 0.24 - 18 0.01796 45.8 -1.11559 -1.11538 -1.09742 0.119E-02 0.23 - 19 0.01807 48.5 -1.11571 -1.11548 -1.09742 0.128E-02 0.24 - 20 0.01809 52.3 -1.11576 -1.11551 -1.09742 0.137E-02 0.23 - 21 0.01805 56.5 -1.11574 -1.11547 -1.09742 0.148E-02 0.30 - 22 0.01795 60.9 -1.11565 -1.11536 -1.09742 0.160E-02 0.30 - 23 0.01779 65.1 -1.11552 -1.11521 -1.09741 0.173E-02 0.31 - 24 0.01760 68.7 -1.11534 -1.11502 -1.09741 0.187E-02 0.28 - 25 0.01740 71.6 -1.11515 -1.11481 -1.09741 0.202E-02 0.23 - 26 0.01719 73.7 -1.11495 -1.11460 -1.09741 0.218E-02 0.24 - 27 0.01700 74.9 -1.11476 -1.11440 -1.09741 0.235E-02 0.24 - 28 0.01683 75.1 -1.11460 -1.11424 -1.09741 0.252E-02 0.24 - 29 0.01670 74.5 -1.11446 -1.11411 -1.09740 0.270E-02 0.24 - 30 0.01661 73.1 -1.11436 -1.11402 -1.09740 0.289E-02 0.24 - 31 0.01656 71.0 -1.11430 -1.11397 -1.09741 0.307E-02 0.23 - 32 0.01651 68.3 -1.11422 -1.11390 -1.09739 0.326E-02 0.23 - 33 0.01658 65.3 -1.11429 -1.11398 -1.09740 0.346E-02 0.22 - 34 0.01675 61.9 -1.11444 -1.11415 -1.09740 0.365E-02 0.23 - 35 0.01702 58.4 -1.11468 -1.11440 -1.09738 0.384E-02 0.22 - 36 0.01763 55.0 -1.11528 -1.11502 -1.09738 0.403E-02 0.22 - 37 0.01849 51.8 -1.11616 -1.11591 -1.09743 0.421E-02 0.23 - 38 0.01897 48.9 -1.11666 -1.11643 -1.09746 0.439E-02 0.23 - 39 0.01859 46.4 -1.11626 -1.11604 -1.09745 0.457E-02 0.22 - 40 0.01745 44.4 -1.11508 -1.11486 -1.09741 0.474E-02 0.23 - 41 0.01611 43.0 -1.11369 -1.11348 -1.09738 0.490E-02 0.23 - 42 0.01516 42.0 -1.11271 -1.11251 -1.09735 0.506E-02 0.23 - 43 0.01498 41.6 -1.11253 -1.11233 -1.09736 0.521E-02 0.23 - 44 0.01550 41.7 -1.11307 -1.11287 -1.09737 0.536E-02 0.23 - 45 0.01649 42.2 -1.11410 -1.11389 -1.09740 0.550E-02 0.23 - 46 0.01752 43.2 -1.11515 -1.11494 -1.09742 0.563E-02 0.23 - 47 0.01827 44.8 -1.11591 -1.11570 -1.09743 0.576E-02 0.24 - 48 0.01864 46.7 -1.11629 -1.11607 -1.09743 0.588E-02 0.24 - 49 0.01862 49.0 -1.11627 -1.11604 -1.09742 0.600E-02 0.23 - 50 0.01841 51.5 -1.11605 -1.11580 -1.09740 0.611E-02 0.23 RESTART INFORMATION WRITTEN ON FILE ./RESTART.1 @@ -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 0.2417 + ION DISPLACEMENT 0.940474E-04 0.917156E-04 + CPU TIME 0.2402 **************************************************************** * * @@ -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 +282,45 @@ **************************************************************** SUBROUTINE CALLS SELF TIME TOTAL TIME AVERAGE MAXIMUM AVERAGE MAXIMUM - cpmd 1 0.00 0.00 13.62 13.62 - mdpt 1 0.00 0.00 13.15 13.15 - mdmain 1 0.02 0.02 13.15 13.15 - forcedr 51 0.00 0.00 12.24 12.24 - forces 51 0.00 0.00 12.24 12.24 - forces_a 51 0.00 0.00 9.59 9.59 - rscpot 51 0.00 0.00 9.59 9.59 - vofrho 52 0.00 0.00 8.17 8.17 - INVFFTN 157 5.11 5.11 5.11 5.11 - VOFRHOB 52 0.21 0.21 5.10 5.10 - FWFFTN 105 3.12 3.12 3.12 3.12 - VOFRHOA 52 0.12 0.12 3.07 3.07 - vpsi 53 0.28 0.28 2.75 2.75 - xcener_new 52 0.19 0.19 2.50 2.50 - mikeu 52 2.31 2.31 2.31 2.31 - rhoofr 51 0.39 0.39 1.73 1.73 - initrun 1 0.00 0.00 0.82 0.82 - rinitwf 1 0.00 0.00 0.82 0.82 - ATOMWF 1 0.00 0.00 0.82 0.82 - potfor 51 0.48 0.48 0.48 0.48 - ATRHO 1 0.35 0.35 0.40 0.40 - ppener 52 0.30 0.30 0.30 0.30 + cpmd 1 0.01 0.01 2.79 2.79 + mdpt 1 0.00 0.00 2.29 2.29 + mdmain 1 0.00 0.00 2.29 2.29 + forcedr 6 0.00 0.00 1.45 1.45 + forces 6 0.00 0.00 1.45 1.45 + vofrho 7 0.00 0.00 1.26 1.26 + forces_a 6 0.00 0.00 1.13 1.13 + rscpot 6 0.00 0.00 1.13 1.13 + VOFRHOB 7 0.02 0.02 0.85 0.85 + 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 + INVFFTN 22 0.73 0.73 0.73 0.73 + xcener_new 7 0.03 0.03 0.49 0.49 + mikeu 7 0.46 0.46 0.46 0.46 + FWFFTN 15 0.44 0.44 0.44 0.44 + vpsi 8 0.04 0.04 0.42 0.42 + VOFRHOA 7 0.01 0.01 0.41 0.41 + ATRHO 1 0.36 0.36 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 0.25 0.25 - EICALC 52 0.18 0.18 0.18 0.18 - dist_ksmat 1 0.00 0.00 0.11 0.11 + loadpa 1 0.01 0.01 0.26 0.26 + rhoofr 6 0.05 0.05 0.20 0.20 + NUMPW 1 0.12 0.12 0.12 0.12 RINFORCE 1 0.00 0.00 0.10 0.10 - NUMPW 1 0.10 0.10 0.10 0.10 loadpa_b 1 0.10 0.10 0.10 0.10 - FORMFN 1 0.10 0.10 0.10 0.10 + dist_ksmat 1 0.00 0.00 0.10 0.10 loadpa_c 1 0.10 0.10 0.10 0.10 + FORMFN 1 0.10 0.10 0.10 0.10 + 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 - ROTATE 152 0.02 0.02 0.02 0.02 - ovlap 152 0.01 0.01 0.02 0.02 - RORTOG 50 0.00 0.00 0.02 0.02 - PHFAC 51 0.01 0.01 0.01 0.01 + 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 0.01 0.01 0.01 0.01 **************************************************************** - CPU TIME : 0 HOURS 0 MINUTES 13.63 SECONDS - ELAPSED TIME : 0 HOURS 0 MINUTES 13.63 SECONDS + CPU TIME : 0 HOURS 0 MINUTES 2.79 SECONDS + ELAPSED TIME : 0 HOURS 0 MINUTES 2.79 SECONDS *** CPMD| SIZE OF THE PROGRAM IS NOT AVAILABLE *** - PROGRAM CPMD ENDED AT: 2016-07-26 14:28:28.366 + PROGRAM CPMD ENDED AT: 2016-07-28 11:16:13.489 diff --git a/test/unittests/cpmd_4.1/md/sample/ENERGIES b/test/unittests/cpmd_4.1/md/sample/ENERGIES new file mode 100644 index 0000000000000000000000000000000000000000..c05b50b1fd5c18dfbd86d81d376785f900660733 --- /dev/null +++ b/test/unittests/cpmd_4.1/md/sample/ENERGIES @@ -0,0 +1,26 @@ + 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 0.24 + 4 0.02592222 412.578 -1.1256188624 -1.1236590243 -1.0977368045 0.137607E-03 0.27 + 5 0.02507375 393.180 -1.1245335482 -1.1226658551 -1.0975921059 0.251896E-03 0.29 + 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 0.24 + 9 0.01428927 71.351 -1.1119610076 -1.1116220739 -1.0973328023 0.755177E-03 0.24 + 10 0.01412005 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0.00077504482656 + 7 0.72193192570691 0.00665625687434 0.00721303188086 0.00065043437225 0.00023204071799 0.00025145019840 -0.09099668775815 -0.00083694955081 -0.00090695704761 + 7 -0.72193192570691 -0.00665625687434 -0.00721303188086 -0.00065043437225 -0.00023204071799 -0.00025145019840 0.09099668775813 0.00083694955081 0.00090695704761 + 10 0.72626584990829 0.00941003227866 0.01019715202805 0.00011553435138 0.00022739762125 0.00024641872984 -0.05932357053850 -0.00048230017030 -0.00052264110802 + 10 -0.72626584990828 -0.00941003227866 -0.01019715202805 -0.00011553435138 -0.00022739762125 -0.00024641872984 0.05932357053847 0.00048230017030 0.00052264110802 + 13 0.72603838813733 0.01212691463322 0.01314129329840 -0.00008020751653 0.00022621309441 0.00024513514017 -0.00455580407816 0.00011486646293 0.00012447860903 + 13 -0.72603838813732 -0.01212691463322 -0.01314129329840 0.00008020751653 -0.00022621309441 -0.00024513514017 0.00455580407814 -0.00011486646294 -0.00012447860903 diff --git a/test/unittests/cpmd_4.1/md/sample/GEOMETRY b/test/unittests/cpmd_4.1/md/sample/GEOMETRY new file mode 100644 index 0000000000000000000000000000000000000000..d83f8e48b3c487ef1edeac2ae1f56c4965f7cbdb --- /dev/null +++ b/test/unittests/cpmd_4.1/md/sample/GEOMETRY @@ -0,0 +1,2 @@ + 0.726038388137 0.012126914633 0.013141293298 -0.000080207517 0.000226213094 0.000245135140 + -0.726038388137 -0.012126914633 -0.013141293298 0.000080207517 -0.000226213094 -0.000245135140 diff --git a/test/unittests/cpmd_4.1/md/sample/GEOMETRY.xyz b/test/unittests/cpmd_4.1/md/sample/GEOMETRY.xyz new file mode 100644 index 0000000000000000000000000000000000000000..36e836beeb8311fdec95fdac68a8dd44fb76532b --- /dev/null +++ b/test/unittests/cpmd_4.1/md/sample/GEOMETRY.xyz @@ -0,0 +1,4 @@ + 2 +GEOMETRY FILE / created by CPMD + H 0.384202969211 0.006417286862 0.006954072935 -0.000042443990 0.000119706814 0.000129719930 + H -0.384202969211 -0.006417286862 -0.006954072935 0.000042443990 -0.000119706814 -0.000129719930 diff --git a/test/unittests/cpmd_4.1/md/sample/LATEST b/test/unittests/cpmd_4.1/md/sample/LATEST new file mode 100644 index 0000000000000000000000000000000000000000..0e4449210602fd9c3a45bd3bc780cd67ad8721b0 --- /dev/null +++ b/test/unittests/cpmd_4.1/md/sample/LATEST @@ -0,0 +1,2 @@ +./RESTART.1 + 1 diff --git a/test/unittests/cpmd_4.1/md/sample/RESTART.1 b/test/unittests/cpmd_4.1/md/sample/RESTART.1 new file mode 100644 index 0000000000000000000000000000000000000000..bec997e2b816df0fad9f8df548b9aa6404dab174 Binary files /dev/null and b/test/unittests/cpmd_4.1/md/sample/RESTART.1 differ diff --git a/test/unittests/cpmd_4.1/md/sample/TRAJEC.xyz b/test/unittests/cpmd_4.1/md/sample/TRAJEC.xyz new file mode 100644 index 0000000000000000000000000000000000000000..319b2164e970b666662d293c7caf1f1ae120f257 --- /dev/null +++ b/test/unittests/cpmd_4.1/md/sample/TRAJEC.xyz @@ -0,0 +1,40 @@ + 2 + STEP: 1 + H 0.371489 0.000511 0.000554 + H -0.371489 -0.000511 -0.000554 + 2 + STEP: 4 + H 0.376437 0.002032 0.002202 + H -0.376437 -0.002032 -0.002202 + 2 + STEP: 7 + H 0.382030 0.003522 0.003817 + H -0.382030 -0.003522 -0.003817 + 2 + STEP: 10 + H 0.384323 0.004980 0.005396 + H -0.384323 -0.004980 -0.005396 + 2 + STEP: 13 + H 0.384203 0.006417 0.006954 + H -0.384203 -0.006417 -0.006954 + 2 + STEP: 1 + H 0.371489 0.000511 0.000554 + H -0.371489 -0.000511 -0.000554 + 2 + STEP: 4 + H 0.376437 0.002032 0.002202 + H -0.376437 -0.002032 -0.002202 + 2 + STEP: 7 + H 0.382030 0.003522 0.003817 + H -0.382030 -0.003522 -0.003817 + 2 + STEP: 10 + H 0.384323 0.004980 0.005396 + H -0.384323 -0.004980 -0.005396 + 2 + STEP: 13 + H 0.384203 0.006417 0.006954 + H -0.384203 -0.006417 -0.006954 diff --git a/test/unittests/cpmd_4.1/md/sample/TRAJECTORY b/test/unittests/cpmd_4.1/md/sample/TRAJECTORY new file mode 100644 index 0000000000000000000000000000000000000000..f1fe4d67d3069c1d5f5cd54e3415464546ff4d7a --- /dev/null +++ b/test/unittests/cpmd_4.1/md/sample/TRAJECTORY @@ -0,0 +1,21 @@ + 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 + 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 + 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 + 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 + 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 + <<<<<< NEW DATA >>>>>> + 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 + 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 + 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 + 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 + 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 diff --git a/test/unittests/cpmd_4.1/md/sample/input.inp b/test/unittests/cpmd_4.1/md/sample/input.inp new file mode 100755 index 0000000000000000000000000000000000000000..a1a082fe6382883b8d1bb563cb4428aaa8ca9976 --- /dev/null +++ b/test/unittests/cpmd_4.1/md/sample/input.inp @@ -0,0 +1,42 @@ +&INFO +isolated hydrogen molecule. +simple molecular dynamics deltat=4au +&END + +&CPMD + MOLECULAR DYNAMICS CP + + TRAJECTORY XYZ SAMPLE FORCES + 3 + + TEMPERATURE + 50.0D0 + + MAXSTEP + 13 + TIMESTEP + 4.0 +&END + +&SYSTEM + SYMMETRY + 1 + ANGSTROM + CELL + 8.00 1.0 1.0 0.0 0.0 0.0 + CUTOFF + 70.0 +&END + +&DFT + FUNCTIONAL LDA +&END + +&ATOMS +*H_MT_LDA.psp + LMAX=S + 2 + 0.371 0.000 0.000 +-0.371 0.000 0.000 +&END + diff --git a/test/unittests/cpmd_4.1/md/ntraj/output.out b/test/unittests/cpmd_4.1/md/sample/output.out similarity index 64% rename from test/unittests/cpmd_4.1/md/ntraj/output.out rename to test/unittests/cpmd_4.1/md/sample/output.out index 2d7249c527d6940aa47276616a237b15cce566e0..4ced26c58bd1632ad036fa21f28ba795d78b758b 100644 --- a/test/unittests/cpmd_4.1/md/ntraj/output.out +++ b/test/unittests/cpmd_4.1/md/sample/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 14:08:55.686 + PROGRAM CPMD STARTED AT: 2016-07-28 13:15:15.642 SETCNST| USING: CODATA 2006 UNITS @@ -29,10 +29,10 @@ THE INPUT FILE IS: input.inp THIS JOB RUNS ON: lenovo700 THE CURRENT DIRECTORY IS: - /home/lauri/Dropbox/nomad-dev/nomad-lab-base/parsers/cpmd/test/unittests/cpmd_4.1/md/ntraj + /home/lauri/Dropbox/nomad-dev/nomad-lab-base/parsers/cpmd/test/unittests/cpmd_4.1/md/sample THE TEMPORARY DIRECTORY IS: - /home/lauri/Dropbox/nomad-dev/nomad-lab-base/parsers/cpmd/test/unittests/cpmd_4.1/md/ntraj - THE PROCESS ID IS: 10413 + /home/lauri/Dropbox/nomad-dev/nomad-lab-base/parsers/cpmd/test/unittests/cpmd_4.1/md/sample + THE PROCESS ID IS: 24005 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: 13 STEPS MAXIMUM NUMBER OF ITERATIONS FOR SC: 10000 STEPS PRINT INTERMEDIATE RESULTS EVERY 10001 STEPS STORE INTERMEDIATE RESULTS EVERY 10001 STEPS @@ -60,8 +60,8 @@ FICTITIOUS ELECTRON MASS: 400.0000 TIME STEP FOR ELECTRONS: 4.0000 TIME STEP FOR IONS: 4.0000 - TRAJECTORIES ARE SAVED ON FILE EVERY 7 STEPS - TRAJEC.xyz IS SAVED ON FILE EVERY 7 STEPS + TRAJECTORIES ARE SAVED ON FILE EVERY 3 STEPS + TRAJEC.xyz IS SAVED ON FILE EVERY 3 STEPS ELECTRON DYNAMICS: THE TEMPERATURE IS NOT CONTROLLED ION DYNAMICS: THE TEMPERATURE IS NOT CONTROLLED SPLINE INTERPOLATION IN G-SPACE FOR PSEUDOPOTENTIAL FUNCTIONS @@ -154,7 +154,7 @@ 1S ALPHA= 1.0000 OCCUPATION= 1.00 - INITIALIZATION TIME: 0.48 SECONDS + INITIALIZATION TIME: 0.51 SECONDS *** MDPT| SIZE OF THE PROGRAM IS NOT AVAILABLE *** *** PHFAC| SIZE OF THE PROGRAM IS NOT AVAILABLE *** @@ -185,11 +185,12 @@ 2 H -0.701088 0.000000 0.000000 **************************************************************** + FILE ENERGIES EXISTS, NEW DATA WILL BE APPENDED ================================================================ == END OF FORCES INITIALIZATION == ================================================================ - TIME FOR INITIALIZATION: 1.12 SECONDS + TIME FOR INITIALIZATION: 1.15 SECONDS **************************************************************** * ATOMIC COORDINATES * @@ -213,56 +214,22 @@ (X) EXCHANGE-CORRELATION ENERGY = -0.57760473 A.U. NFI EKINC TEMPP EKS ECLASSIC EHAM DIS TCPU - 1 0.00473 110.1 -1.10235 -1.10183 -1.09710 0.289E-05 0.25 - 2 0.01424 232.5 -1.11287 -1.11176 -1.09752 0.182E-04 0.26 - 3 0.02229 352.0 -1.12169 -1.12002 -1.09773 0.596E-04 0.25 - 4 0.02592 412.6 -1.12562 -1.12366 -1.09774 0.138E-03 0.25 - 5 0.02507 393.2 -1.12453 -1.12267 -1.09759 0.252E-03 0.41 - 6 0.02170 311.4 -1.12061 -1.11913 -1.09743 0.390E-03 0.35 - 7 0.01807 208.9 -1.11639 -1.11540 -1.09733 0.531E-03 0.36 - 8 0.01550 123.5 -1.11340 -1.11281 -1.09731 0.656E-03 0.37 - 9 0.01429 71.4 -1.11196 -1.11162 -1.09733 0.755E-03 0.37 - 10 0.01412 48.7 -1.11172 -1.11149 -1.09737 0.826E-03 0.39 - 11 0.01455 43.2 -1.11215 -1.11194 -1.09739 0.876E-03 0.33 - 12 0.01522 44.1 -1.11284 -1.11263 -1.09741 0.911E-03 0.26 + 1 0.00473 110.1 -1.10235 -1.10183 -1.09710 0.289E-05 0.24 + FILE TRAJECTORY EXISTS, NEW DATA WILL BE APPENDED + FILE TRAJEC.xyz EXISTS, NEW DATA WILL BE APPENDED + FILE FTRAJECTORY EXISTS, NEW DATA WILL BE APPENDED + 2 0.01424 232.5 -1.11287 -1.11176 -1.09752 0.182E-04 0.23 + 3 0.02229 352.0 -1.12169 -1.12002 -1.09773 0.596E-04 0.23 + 4 0.02592 412.6 -1.12562 -1.12366 -1.09774 0.138E-03 0.23 + 5 0.02507 393.2 -1.12453 -1.12267 -1.09759 0.252E-03 0.23 + 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 0.22 + 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 0.25 13 0.01592 45.5 -1.11355 -1.11334 -1.09742 0.942E-03 0.24 - 14 0.01655 45.6 -1.11419 -1.11397 -1.09742 0.975E-03 0.24 - 15 0.01707 44.7 -1.11470 -1.11449 -1.09742 0.101E-02 0.24 - 16 0.01747 44.0 -1.11509 -1.11489 -1.09742 0.106E-02 0.26 - 17 0.01776 44.2 -1.11539 -1.11518 -1.09742 0.112E-02 0.35 - 18 0.01796 45.8 -1.11559 -1.11538 -1.09742 0.119E-02 0.35 - 19 0.01807 48.5 -1.11571 -1.11548 -1.09742 0.128E-02 0.34 - 20 0.01809 52.3 -1.11576 -1.11551 -1.09742 0.137E-02 0.32 - 21 0.01805 56.5 -1.11574 -1.11547 -1.09742 0.148E-02 0.23 - 22 0.01795 60.9 -1.11565 -1.11536 -1.09742 0.160E-02 0.23 - 23 0.01779 65.1 -1.11552 -1.11521 -1.09741 0.173E-02 0.23 - 24 0.01760 68.7 -1.11534 -1.11502 -1.09741 0.187E-02 0.23 - 25 0.01740 71.6 -1.11515 -1.11481 -1.09741 0.202E-02 0.23 - 26 0.01719 73.7 -1.11495 -1.11460 -1.09741 0.218E-02 0.23 - 27 0.01700 74.9 -1.11476 -1.11440 -1.09741 0.235E-02 0.23 - 28 0.01683 75.1 -1.11460 -1.11424 -1.09741 0.252E-02 0.23 - 29 0.01670 74.5 -1.11446 -1.11411 -1.09740 0.270E-02 0.22 - 30 0.01661 73.1 -1.11436 -1.11402 -1.09740 0.289E-02 0.23 - 31 0.01656 71.0 -1.11430 -1.11397 -1.09741 0.307E-02 0.24 - 32 0.01651 68.3 -1.11422 -1.11390 -1.09739 0.326E-02 0.22 - 33 0.01658 65.3 -1.11429 -1.11398 -1.09740 0.346E-02 0.23 - 34 0.01675 61.9 -1.11444 -1.11415 -1.09740 0.365E-02 0.23 - 35 0.01702 58.4 -1.11468 -1.11440 -1.09738 0.384E-02 0.22 - 36 0.01763 55.0 -1.11528 -1.11502 -1.09738 0.403E-02 0.23 - 37 0.01849 51.8 -1.11616 -1.11591 -1.09743 0.421E-02 0.22 - 38 0.01897 48.9 -1.11666 -1.11643 -1.09746 0.439E-02 0.22 - 39 0.01859 46.4 -1.11626 -1.11604 -1.09745 0.457E-02 0.24 - 40 0.01745 44.4 -1.11508 -1.11486 -1.09741 0.474E-02 0.23 - 41 0.01611 43.0 -1.11369 -1.11348 -1.09738 0.490E-02 0.23 - 42 0.01516 42.0 -1.11271 -1.11251 -1.09735 0.506E-02 0.22 - 43 0.01498 41.6 -1.11253 -1.11233 -1.09736 0.521E-02 0.23 - 44 0.01550 41.7 -1.11307 -1.11287 -1.09737 0.536E-02 0.23 - 45 0.01649 42.2 -1.11410 -1.11389 -1.09740 0.550E-02 0.22 - 46 0.01752 43.2 -1.11515 -1.11494 -1.09742 0.563E-02 0.22 - 47 0.01827 44.8 -1.11591 -1.11570 -1.09743 0.576E-02 0.23 - 48 0.01864 46.7 -1.11629 -1.11607 -1.09743 0.588E-02 0.23 - 49 0.01862 49.0 -1.11627 -1.11604 -1.09742 0.600E-02 0.23 - 50 0.01841 51.5 -1.11605 -1.11580 -1.09740 0.611E-02 0.22 RESTART INFORMATION WRITTEN ON FILE ./RESTART.1 @@ -271,17 +238,17 @@ **************************************************************** 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 0.017049 0.542336E-02 + IONIC TEMPERATURE 184.3894 136.470 + DENSITY FUNCTIONAL ENERGY -1.115360 0.608996E-02 + CLASSICAL ENERGY -1.114484 0.556736E-02 + CONSERVED ENERGY -1.097435 0.168835E-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 0.2600 + ION DISPLACEMENT 0.489073E-03 0.348590E-03 + CPU TIME 0.2319 **************************************************************** * * @@ -292,8 +259,8 @@ **************************************************************** * ATOMIC COORDINATES * **************************************************************** - 1 H 0.740084 0.045947 0.049790 - 2 H -0.740084 -0.045947 -0.049790 + 1 H 0.726038 0.012127 0.013141 + 2 H -0.726038 -0.012127 -0.013141 **************************************************************** @@ -301,20 +268,20 @@ ELECTRONIC GRADIENT: - MAX. COMPONENT = 1.39929E-02 NORM = 2.08955E-03 + MAX. COMPONENT = 2.44256E-02 NORM = 2.10354E-03 TOTAL INTEGRATED ELECTRONIC DENSITY - IN G-SPACE = 1.9999999999 - IN R-SPACE = 1.9999999999 + IN G-SPACE = 2.0000000000 + IN R-SPACE = 2.0000000000 - (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 = -1.11355483 A.U. + (K) KINETIC ENERGY = 1.15853626 A.U. + (E1=A-S+R) ELECTROSTATIC ENERGY = -0.48667158 A.U. (S) ESELF = 0.66490380 A.U. - (R) ESR = 0.14497305 A.U. - (L) LOCAL PSEUDOPOTENTIAL ENERGY = -1.04064388 A.U. + (R) ESR = 0.15567016 A.U. + (L) LOCAL PSEUDOPOTENTIAL ENERGY = -1.11134504 A.U. (N) N-L PSEUDOPOTENTIAL ENERGY = 0.00000000 A.U. - (X) EXCHANGE-CORRELATION ENERGY = -0.63585977 A.U. + (X) EXCHANGE-CORRELATION ENERGY = -0.67407448 A.U. **************************************************************** @@ -327,47 +294,48 @@ **************************************************************** SUBROUTINE CALLS SELF TIME TOTAL TIME AVERAGE MAXIMUM AVERAGE MAXIMUM - cpmd 1 0.00 0.00 14.60 14.60 - mdpt 1 0.00 0.00 14.13 14.13 - mdmain 1 0.01 0.01 14.13 14.13 - forcedr 51 0.00 0.00 13.22 13.22 - forces 51 0.00 0.00 13.22 13.22 - forces_a 51 0.00 0.00 10.36 10.36 - rscpot 51 0.00 0.00 10.36 10.36 - vofrho 52 0.00 0.00 8.82 8.82 - INVFFTN 157 5.48 5.48 5.48 5.48 - VOFRHOB 52 0.27 0.27 5.43 5.43 - VOFRHOA 52 0.12 0.12 3.39 3.39 - FWFFTN 105 3.39 3.39 3.39 3.39 - vpsi 53 0.29 0.29 2.94 2.94 - xcener_new 52 0.21 0.21 2.61 2.61 - mikeu 52 2.39 2.39 2.39 2.39 - rhoofr 51 0.44 0.44 1.88 1.88 - initrun 1 0.00 0.00 0.83 0.83 - rinitwf 1 0.00 0.00 0.83 0.83 - ATOMWF 1 0.00 0.00 0.83 0.83 - potfor 51 0.56 0.56 0.56 0.56 - ATRHO 1 0.36 0.36 0.40 0.40 - ppener 52 0.32 0.32 0.32 0.32 - rinit 1 0.00 0.00 0.26 0.26 - rggen 1 0.01 0.01 0.26 0.26 + cpmd 1 0.01 0.01 4.67 4.67 + mdpt 1 0.00 0.00 4.17 4.17 + mdmain 1 0.00 0.00 4.17 4.17 + forcedr 14 0.00 0.00 3.29 3.29 + forces 14 0.00 0.00 3.29 3.29 + forces_a 14 0.00 0.00 2.58 2.58 + rscpot 14 0.00 0.00 2.58 2.58 + vofrho 15 0.00 0.00 2.46 2.46 + VOFRHOB 15 0.06 0.06 1.56 1.56 + INVFFTN 46 1.47 1.47 1.47 1.47 + FWFFTN 31 0.92 0.92 0.92 0.92 + VOFRHOA 15 0.04 0.04 0.90 0.90 + initrun 1 0.00 0.00 0.86 0.86 + rinitwf 1 0.00 0.00 0.86 0.86 + ATOMWF 1 0.00 0.00 0.86 0.86 + xcener_new 15 0.06 0.06 0.83 0.83 + vpsi 16 0.08 0.08 0.81 0.81 + mikeu 15 0.77 0.77 0.77 0.77 + rhoofr 14 0.10 0.10 0.46 0.46 + ATRHO 1 0.36 0.36 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 - EICALC 52 0.19 0.19 0.19 0.19 - RINFORCE 1 0.00 0.00 0.10 0.10 - loadpa_b 1 0.10 0.10 0.10 0.10 - NUMPW 1 0.10 0.10 0.10 0.10 - dist_ksmat 1 0.00 0.00 0.10 0.10 - loadpa_c 1 0.10 0.10 0.10 0.10 + potfor 14 0.13 0.13 0.13 0.13 + NUMPW 1 0.11 0.11 0.11 0.11 + dist_ksmat 1 0.00 0.00 0.11 0.11 + loadpa_b 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_c 1 0.10 0.10 0.10 0.10 + ppener 15 0.09 0.09 0.09 0.09 + EICALC 15 0.05 0.05 0.05 0.05 loadpa_a 1 0.04 0.04 0.04 0.04 - POSUPA 50 0.00 0.00 0.02 0.02 - PHFAC 51 0.02 0.02 0.02 0.02 - ovlap 152 0.01 0.01 0.02 0.02 - RORTOG 50 0.00 0.00 0.02 0.02 + PUTPS 1 0.01 0.01 0.01 0.01 + fftprp 1 0.01 0.01 0.01 0.01 + PHFAC 14 0.01 0.01 0.01 0.01 + ovlap 41 0.00 0.00 0.01 0.01 + POSUPA 13 0.00 0.00 0.01 0.01 **************************************************************** - CPU TIME : 0 HOURS 0 MINUTES 14.61 SECONDS - ELAPSED TIME : 0 HOURS 0 MINUTES 14.61 SECONDS + CPU TIME : 0 HOURS 0 MINUTES 4.68 SECONDS + ELAPSED TIME : 0 HOURS 0 MINUTES 4.68 SECONDS *** CPMD| SIZE OF THE PROGRAM IS NOT AVAILABLE *** - PROGRAM CPMD ENDED AT: 2016-07-26 14:09:10.292 + PROGRAM CPMD ENDED AT: 2016-07-28 13:15:20.318 diff --git a/test/unittests/cpmd_4.1/md/sample/run.sh b/test/unittests/cpmd_4.1/md/sample/run.sh new file mode 100755 index 0000000000000000000000000000000000000000..74ce0ca5a55a21a25741d586bcf4cb42c8f14590 --- /dev/null +++ b/test/unittests/cpmd_4.1/md/sample/run.sh @@ -0,0 +1,3 @@ +export CPMD_PP_LIBRARY_PATH=../../ +export OMP_NUM_THREADS=1 +cpmd41 input.inp > output.out diff --git a/test/unittests/cpmd_4.1/run_tests.py b/test/unittests/cpmd_4.1/run_tests.py index 9178139284edaf9b1b8e33e1cb9c20492eee514b..b8f032d214660f3ed394ae868f0d80f624e85f85 100644 --- a/test/unittests/cpmd_4.1/run_tests.py +++ b/test/unittests/cpmd_4.1/run_tests.py @@ -487,6 +487,26 @@ class TestMD(unittest.TestCase): self.assertTrue(np.array_equal(result[0, :], expected_start)) self.assertTrue(np.array_equal(result[-1, :], expected_end)) + def test_atom_forces(self): + result = self.results["atom_forces"] + expected_start = convert_unit( + np.array([ + [0.15293653991241, -0.00036559789218, -0.00039617900820], + [-0.15293653991238, 0.00036559789217, 0.00039617900820], + ]), + "forceAu" + ) + expected_end = convert_unit( + np.array([ + [-0.03595092814462, -0.00079338139843, -0.00085974499854], + [0.03595092814462, 0.00079338139843, 0.00085974499854], + ]), + "forceAu" + ) + + 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)) @@ -605,6 +625,65 @@ class TestMDTrajFormats(unittest.TestCase): 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_ftrajectory(self): + results = get_results("md/ftrajectory", "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)) + + +#=============================================================================== +class TestMDPrintSettings(unittest.TestCase): + """Test that the print settings are interpreted corrrectly. + """ + def test_range(self): + """If a range is specified, then the trajectory/veocity/forces cannot + be read from the TRAJECTORY or FTRAJECTORY files. Only if a + TRAJEC.xyz/dcd file exists can the trajectory be read, because it is + not affected by range. + """ + results = get_results("md/range", "section_run") + results["atom_positions"] + with self.assertRaises(LookupError): + results["atom_velocities"] + with self.assertRaises(LookupError): + results["atom_forces"] + + def test_sample(self): + results = get_results("md/sample", "section_run") + + # Seet that the pos, vel and forces are associated with the correct scc + sccs = results["section_single_configuration_calculation"] + systems = results["section_system"] + + for i_scc, scc in sccs.items(): + ref = scc["single_configuration_calculation_to_system_ref"][0] + system = systems[ref] + pos = system["atom_positions"] + vel = system["atom_velocities"] + forces = scc["atom_forces"] + if i_scc % 3 == 0: + self.assertNotEqual(pos, None) + self.assertNotEqual(vel, None) + self.assertNotEqual(forces, None) + else: + self.assertEqual(pos, None) + self.assertEqual(vel, None) + self.assertEqual(forces, None) # #=============================================================================== # class TestErrors(unittest.TestCase): @@ -1076,5 +1155,6 @@ if __name__ == '__main__': suites.append(unittest.TestLoader().loadTestsFromTestCase(TestInputParser)) suites.append(unittest.TestLoader().loadTestsFromTestCase(TestMD)) suites.append(unittest.TestLoader().loadTestsFromTestCase(TestMDTrajFormats)) + suites.append(unittest.TestLoader().loadTestsFromTestCase(TestMDPrintSettings)) alltests = unittest.TestSuite(suites) unittest.TextTestRunner(verbosity=0).run(alltests)