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parser-cp2k
Commit 4961e40b authored by Lauri Himanen's avatar Lauri Himanen
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Fixed issue with restarted calculations, fixed bugs in reading MD files with... 

Fixed issue with restarted calculations, fixed bugs in reading MD files with non-unity print frequencies.
parent d361b1ad
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Showing with 172204 additions and 194 deletions
parser/parser-cp2k/cp2kparser/parser.py
View file @ 4961e40b
......@@ -32,12 +32,15 @@ class CP2KParser(ParserInterface):
# this information.
regex_version = re.compile(r" CP2K\| version string:\s+CP2K version ([\d\.]+)")
regex_run_type = re.compile(r"\s+GLOBAL\| Run type\s+(.+)")
n_lines = 50
n_lines = 100
version_id = None
run_type = None
with open(self.parser_context.main_file, 'r') as outputfile:
for i_line in range(n_lines):
line = next(outputfile)
try:
line = next(outputfile)
except StopIteration:
break
result_version = regex_version.match(line)
result_run_type = regex_run_type.match(line)
if result_version:
......
parser/parser-cp2k/cp2kparser/versions/cp2k262/inputparser.py
View file @ 4961e40b
......@@ -70,20 +70,16 @@ class CP2KInputParser(AbstractBaseParser):
def parse(self, filepath):
#=======================================================================
# Preprocess to spell out variables and to include stuff from other
# files
self.preprocess_input(filepath)
#=======================================================================
# Gather the information from the input file
self.fill_input_tree(filepath)
#=======================================================================
# Parse everything in the input to cp2k specific metadata
self.fill_metadata()
#=======================================================================
# Parse the used XC_functionals and their parameters
xc = self.input_tree.get_section("FORCE_EVAL/DFT/XC/XC_FUNCTIONAL")
if xc is not None:
......
regtests/cp2k_2.6.2/errors/short_main_file/unittest.out 0 → 100644
View file @ 4961e40b
*******************************************************************************
* RESTART INFORMATION *
*******************************************************************************
* *
* RESTART FILE NAME: ./md_trajectory-restart-1.restart *
* *
* RESTARTED QUANTITIES: *
* CELL *
* COORDINATES *
* RANDOM NUMBER GENERATOR *
* VELOCITIES *
* MD COUNTERS *
* MD AVERAGES *
* BAROSTAT *
* THERMOSTAT OF BAROSTAT *
* PARTICLE THERMOSTAT *
* REAL TIME PROPAGATION *
* PINT BEAD POSITIONS *
* PINT BEAD VELOCITIES *
* PINT NOSE THERMOSTAT *
* PINT GLE THERMOSTAT *
* HELIUM BEAD POSITIONS *
* HELIUM PERMUTATION STATE *
* HELIUM FORCES ON SOLUTE *
* HELIUM RNG STATE *
*******************************************************************************
DBCSR| Multiplication driver BLAS
DBCSR| Multrec recursion limit 512
DBCSR| Multiplication stack size 1000
DBCSR| Maximum elements for images UNLIMITED
DBCSR| Randmat seed 12341313
DBCSR| Multiplication size stacks 3
DBCSR| Use MPI memory allocation T
DBCSR| Use RMA algorithm F
DBCSR| Use Communication thread T
DBCSR| Communication thread load 87
**** **** ****** ** PROGRAM STARTED AT 2017-06-22 08:42:05.697
***** ** *** *** ** PROGRAM STARTED ON mpp2r04c06s08
** **** ****** PROGRAM STARTED BY root ;-)
***** ** ** ** ** PROGRAM PROCESS ID 19346
**** ** ******* ** PROGRAM STARTED IN /naslx/projects/t3881/ga68gak2/SoS17/
regtests/cp2k_2.6.2/geo_opt/geometry_formats/default/H2O-geometry-pos-1.xyz 0 → 100644
View file @ 4961e40b
3
i = 1, E = -17.1547973121
O 12.2353220000 1.3766420000 10.8698800000
H 12.4175624065 2.2362390825 11.2616392180
H 11.9271777126 1.5723402996 10.0115089094
3
i = 2, E = -17.1952478380
O 12.2353220000 1.3766420000 10.8698800000
H 12.4611837365 2.2315454308 11.3332902926
H 11.9990446426 1.5776159715 10.0384156630
3
i = 3, E = -17.2105811202
O 12.2353220000 1.3766420000 10.8698800000
H 12.4888432333 2.2313057818 11.3363388157
H 11.9954084316 1.5758795771 10.0014338600
3
i = 4, E = -17.2111555704
O 12.2353220000 1.3766420000 10.8698800000
H 12.4964443436 2.2308405984 11.3356275380
H 11.9974956117 1.5745995415 10.0050279862
3
i = 5, E = -17.2111711743
O 12.2353220000 1.3766420000 10.8698800000
H 12.4957585748 2.2307147530 11.3354424217
H 11.9976076309 1.5747583571 10.0062478081
3
i = 6, E = -17.2111712050
O 12.2353220000 1.3766420000 10.8698800000
H 12.4957992354 2.2307217848 11.3354453760
H 11.9975767140 1.5747992013 10.0062527771
3
i = 7, E = -17.2111764458
O 12.2353220000 1.3766420000 10.8698800000
H 12.4957995882 2.2307218433 11.3354453867
H 11.9975764125 1.5747996320 10.0062529540
regtests/cp2k_2.6.2/geo_opt/geometry_formats/default/geo_opt.inp 0 → 100644
View file @ 4961e40b
&GLOBAL
PROJECT H2O
RUN_TYPE GEO_OPT
PRINT_LEVEL MEDIUM
&END GLOBAL
&FORCE_EVAL
METHOD QS
&SUBSYS
&CELL
ABC 12.4138 12.4138 12.4138
&END CELL
&COORD
O 12.235322 1.376642 10.869880
H 12.415139 2.233125 11.257611
H 11.922476 1.573799 9.986994
&END COORD
&KIND H
BASIS_SET DZVP-GTH-PADE
POTENTIAL GTH-PADE-q1
&END KIND
&KIND O
BASIS_SET DZVP-GTH-PADE
POTENTIAL GTH-PADE-q6
&END KIND
&END SUBSYS
&DFT
BASIS_SET_FILE_NAME ../../../BASIS_SET
POTENTIAL_FILE_NAME ../../../GTH_POTENTIALS
&QS
EPS_DEFAULT 1.0E-7
&END QS
&MGRID
CUTOFF 100
NGRIDS 3
REL_CUTOFF 20
&END MGRID
&SCF
SCF_GUESS ATOMIC
EPS_SCF 1.0E-05
MAX_SCF 200
&DIAGONALIZATION T
ALGORITHM STANDARD
&END DIAGONALIZATION
&MIXING T
ALPHA 0.5
METHOD PULAY_MIXING
NPULAY 5
&END MIXING
&PRINT
&RESTART OFF
&END RESTART
&END PRINT
&END SCF
&XC
&XC_FUNCTIONAL PADE
&END XC_FUNCTIONAL
&END XC
&END DFT
&END FORCE_EVAL
&MOTION
&GEO_OPT
TYPE MINIMIZATION
MAX_DR 1.0E-03
MAX_FORCE 1.0E-03
RMS_DR 1.0E-03
RMS_FORCE 1.0E-03
MAX_ITER 200
OPTIMIZER CG
&CG
MAX_STEEP_STEPS 0
RESTART_LIMIT 9.0E-01
&END CG
&END GEO_OPT
&CONSTRAINT
&FIXED_ATOMS
COMPONENTS_TO_FIX XYZ
LIST 1
&END FIXED_ATOMS
&END CONSTRAINT
&PRINT
&TRAJECTORY
FILENAME geometry
&END TRAJECTORY
&END PRINT
&END MOTION
regtests/cp2k_2.6.2/md/print_settings/H2O-32-1.cell 0 → 100644
View file @ 4961e40b
# Step Time [fs] Ax [Angstrom] Ay [Angstrom] Az [Angstrom] Bx [Angstrom] By [Angstrom] Bz [Angstrom] Cx [Angstrom] Cy [Angstrom] Cz [Angstrom] Volume [Angstrom^3]
0 0.000 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 956.4868456940
1 0.500 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 956.4868456940
2 1.000 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 956.4868456940
3 1.500 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 956.4868456940
4 2.000 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 956.4868456940
5 2.500 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 956.4868456940
6 3.000 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 956.4868456940
7 3.500 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 956.4868456940
8 4.000 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 956.4868456940
9 4.500 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 956.4868456940
10 5.000 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 956.4868456940
regtests/cp2k_2.6.2/md/print_settings/H2O-32-1.ener 0 → 100644
View file @ 4961e40b
# Step Nr. Time[fs] Kin.[a.u.] Temp[K] Pot.[a.u.] Cons Qty[a.u.] UsedTime[s]
0 0.000000 0.007125335 300.000000000 -34.330396471 -34.323271136 0.000000000
3 1.500000 0.004815598 202.752506973 -34.327998978 -34.323183380 1.837741619
6 3.000000 0.005184860 218.299664775 -34.328412394 -34.323227533 1.804586368
9 4.500000 0.005371243 226.146979313 -34.328598255 -34.323227013 1.819971947
regtests/cp2k_2.6.2/md/print_settings/H2O-32-1.restart 0 → 100644
View file @ 4961e40b
# Version information for this restart file
# current date 2017-10-31 17:50:49.271
# current working dir /home/lauri/Dropbox/nomad-dev/WP1/nomad-lab-base/parsers/cp2k/regtests/cp2k_2.6.2/md/print_settings
# Program compiled at ma 13.6.2016 11.25.35 +0300
# Program compiled on lenovo700
# Program compiled for Linux-x86-64-gfortran_basic
# Source code revision number svn:15893
&GLOBAL
PRINT_LEVEL MEDIUM
PROJECT_NAME H2O-32
RUN_TYPE MD
&END GLOBAL
&MOTION
&MD
ENSEMBLE NVE
STEPS 10
TIMESTEP 4.9999999999999994E-01
STEP_START_VAL 10
TIME_START_VAL 4.9999999999999982E+00
ECONS_START_VAL -3.4323271136444127E+01
TEMPERATURE 3.0000000000000000E+02
&AVERAGES T
&RESTART_AVERAGES
ITIMES_START 1
AVECPU 2.0361026731996392E+00
AVEHUGONIOT 0.0000000000000000E+00
AVETEMP_BARO 0.0000000000000000E+00
AVEPOT -3.4328507994982211E+01
AVEKIN 5.2904284572055657E-03
AVETEMP 2.2274442444397368E+02
AVEKIN_QM 0.0000000000000000E+00
AVETEMP_QM 0.0000000000000000E+00
AVEVOL 6.4546932590671622E+03
AVECELL_A 1.8619093642095663E+01
AVECELL_B 1.8619093642095663E+01
AVECELL_C 1.8619093642095663E+01
AVEALPHA 9.0000000000000000E+01
AVEBETA 9.0000000000000000E+01
AVEGAMMA 9.0000000000000000E+01
AVE_ECONS 2.6851773896551094E+00
AVE_PRESS -4.5584290676900036E+02
AVE_PXX -1.4444922892417906E+03
&END RESTART_AVERAGES
&END AVERAGES
&PRINT
&ENERGY SILENT
&EACH
MD 3
&END EACH
&END ENERGY
&END PRINT
&END MD
&PRINT
&TRAJECTORY SILENT
ADD_LAST NUMERIC
&EACH
MD 3
&END EACH
&END TRAJECTORY
&CELL MEDIUM
&END CELL
&VELOCITIES SILENT
ADD_LAST NUMERIC
&EACH
MD 3
&END EACH
&END VELOCITIES
&FORCES SILENT
ADD_LAST NUMERIC
&EACH
MD 3
&END EACH
&END FORCES
&STRESS MEDIUM
&END STRESS
&END PRINT
&END MOTION
&FORCE_EVAL
METHOD QS
STRESS_TENSOR ANALYTICAL
&DFT
BASIS_SET_FILE_NAME ../../BASIS_SET
POTENTIAL_FILE_NAME ../../GTH_POTENTIALS
&SCF
SCF_GUESS ATOMIC
&PRINT
&RESTART OFF
&END RESTART
&END PRINT
&END SCF
&QS
EPS_DEFAULT 9.9999999999999998E-13
EXTRAPOLATION PS
EXTRAPOLATION_ORDER 3
&END QS
&MGRID
CUTOFF 2.0000000000000000E+02
REL_CUTOFF 3.0000000000000000E+01
&END MGRID
&XC
DENSITY_CUTOFF 1.0000000000000000E-10
GRADIENT_CUTOFF 1.0000000000000000E-10
TAU_CUTOFF 1.0000000000000000E-10
&XC_FUNCTIONAL NO_SHORTCUT
&PADE T
&END PADE
&END XC_FUNCTIONAL
&END XC
&END DFT
&SUBSYS
&CELL
A 9.8528000000000002E+00 0.0000000000000000E+00 0.0000000000000000E+00
B 0.0000000000000000E+00 9.8528000000000002E+00 0.0000000000000000E+00
C 0.0000000000000000E+00 0.0000000000000000E+00 9.8528000000000002E+00
MULTIPLE_UNIT_CELL 1 1 1
&END CELL
&COORD
O 2.2916014875365640E+00 9.1431763259661576E+00 5.0868100687592195E+00
O 1.2366834077559758E+00 2.4077552776368130E+00 7.7630044422558484E+00
H 1.6909790671242531E+00 9.8235337924223973E+00 5.5042564093642099E+00
H 3.1130341663852827E+00 9.0372111809879208E+00 5.6100739746439290E+00
H 5.6520704776688990E-01 3.0441761067190227E+00 8.1734257298704680E+00
H 1.8669280879200694E+00 2.9877213524408646E+00 7.2364955946421139E+00
&END COORD
&VELOCITY
1.6002631268526558E-04 -3.8330777538316441E-05 1.5366243314343522E-05
-1.2693807804078539E-04 -5.1514517930570524E-07 -7.2621411450565928E-05
1.7709292292150271E-05 -3.2578140177274173E-04 -2.5785159470930532E-05
-1.5067044782202973E-03 -1.7004890732398277E-04 -3.6516053711636609E-04
3.0792641968561290E-05 6.8867188906561244E-04 8.4313211607861993E-04
7.4246807566395452E-04 3.6141271394655056E-04 5.7490894909811852E-04
&END VELOCITY
&KIND H
BASIS_SET DZVP-GTH-PADE
POTENTIAL GTH-PADE-q1
&BASIS
2
1 0 0 4 2
0.8374435000900000E+01 -0.2389437320000000E-01 0.0000000000000000E+00
0.1805868146000000E+01 -0.1397943259000000E+00 0.0000000000000000E+00
0.4852531032000000E+00 -0.2530970874000000E+00 0.0000000000000000E+00
0.1658235797000000E+00 -0.6955307423000000E+00 0.1000000000000000E+01
2 1 1 1 1
0.7000000000000000E+00 0.1000000000000000E+01
# Basis set name: DZVP-GTH-PADE for symbol: H
# Basis set read from the basis set filename: ../../BASIS_SET
&END BASIS
&POTENTIAL
1
0.2000000000000000E+00 2 -0.4180236800000000E+01 0.7250748200000000E+00
0
# Potential name: GTH-PADE-Q1 for symbol: H
# Potential read from the potential filename: ../../GTH_POTENTIALS
&END POTENTIAL
&END KIND
&KIND O
BASIS_SET DZVP-GTH-PADE
POTENTIAL GTH-PADE-q6
&BASIS
2
2 0 1 4 2 2
0.8304404230499999E+01 0.1510163077000000E+00 0.0000000000000000E+00 -0.9956780470000000E-01 0.0000000000000000E+00
0.2457945246100000E+01 -0.3931938740000000E-01 0.0000000000000000E+00 -0.3011430914000000E+00 0.0000000000000000E+00
0.7597363524000000E+00 -0.6971729792000000E+00 0.0000000000000000E+00 -0.4750852730000000E+00 0.0000000000000000E+00
0.2136387585000000E+00 -0.3841125601000000E+00 0.1000000000000000E+01 -0.3798775565000000E+00 0.1000000000000000E+01
3 2 2 1 1
0.8000000000000000E+00 0.1000000000000000E+01
# Basis set name: DZVP-GTH-PADE for symbol: O
# Basis set read from the basis set filename: ../../BASIS_SET
&END BASIS
&POTENTIAL
2 4
0.2476208600000000E+00 2 -0.1658031797000000E+02 0.2395700920000000E+01
2
0.2217861400000000E+00 1 0.1826691718000000E+02
0.2568289000000000E+00 0
# Potential name: GTH-PADE-Q6 for symbol: O
# Potential read from the potential filename: ../../GTH_POTENTIALS
&END POTENTIAL
&END KIND
&TOPOLOGY
NUMBER_OF_ATOMS 6
MULTIPLE_UNIT_CELL 1 1 1
&END TOPOLOGY
&END SUBSYS
&END FORCE_EVAL
regtests/cp2k_2.6.2/md/print_settings/H2O-32-1.stress 0 → 100644
View file @ 4961e40b
# Step Time [fs] xx [bar] xy [bar] xz [bar] yx [bar] yy [bar] yz [bar] zx [bar] zy [bar] zz [bar]
0 0.000 3188.5381565467 -910.2707492147 -386.3720503451 -910.2707492147 1595.9782110598 -95.0502014410 -386.3720503451 -95.0502014410 1388.9989761559
1 0.500 2768.9454897172 -1030.8010041752 -1513.5283901605 -1030.8010041752 2170.9082578351 47.6901641714 -1513.5283901605 47.6901641714 1394.4156422630
2 1.000 2027.6966344004 -964.6037791919 -2366.5620483656 -964.6037791919 2426.0161743730 188.1902150437 -2366.5620483656 188.1902150437 1220.5743970236
3 1.500 1001.4586030693 -707.6691243940 -2822.0793506936 -707.6691243940 2310.4643572158 298.8886807875 -2822.0793506936 298.8886807875 886.4284757691
4 2.000 -223.0759992619 -289.5766423965 -2838.1956670980 -289.5766423965 1838.3430325624 354.9795374366 -2838.1956670980 354.9795374366 428.7697054591
5 2.500 -1516.4620326882 228.5480546051 -2450.2192168589 228.5480546051 1087.8444542250 342.5326078152 -2450.2192168589 342.5326078152 -92.3575964328
6 3.000 -2718.1530466205 766.6607468116 -1746.3712491068 766.6607468116 178.2562259178 261.5771290575 -1746.3712491068 261.5771290575 -603.1238347886
7 3.500 -3655.8283071244 1243.5845231699 -836.4733793151 1243.5845231699 -760.6918189509 123.9547839784 -836.4733793151 123.9547839784 -1032.7376376763
8 4.000 -4180.4600166230 1592.2212773121 173.2273916320 1592.2212773121 -1611.4078109125 -51.2035587799 173.2273916320 -51.2035587799 -1323.8694355803
9 4.500 -4207.7062193525 1768.3572863524 1188.7544063041 1768.3572863524 -2279.0968250839 -241.6347039653 1188.7544063041 -241.6347039653 -1433.8355926924
10 5.000 -3741.3379979342 1754.0704259022 2125.6524791911 1754.0704259022 -2698.5126532575 -423.9403447230 2125.6524791911 -423.9403447230 -1336.7518279209
regtests/cp2k_2.6.2/md/print_settings/H2O-32-frc-1.xyz 0 → 100644
View file @ 4961e40b
6
i = 0, time = 0.000, E = -34.3303964710
O -0.0051113524 -0.0116682698 -0.0173716502
O 0.0031727484 -0.0214847893 0.0029206097
H -0.0111148574 0.0131903452 0.0096270538
H 0.0162471668 -0.0006417640 0.0094661991
H -0.0139497666 0.0106352478 0.0061900539
H 0.0114080321 0.0105987085 -0.0115332886
6
i = 3, time = 1.500, E = -34.3279989781
O 0.0301292557 -0.0149239480 0.0029973834
O 0.0129491199 -0.0427906935 -0.0000589924
H -0.0044049345 0.0095586397 0.0110741967
H -0.0277182746 0.0053527699 -0.0114121937
H -0.0306922598 0.0256759188 0.0156813735
H 0.0181696678 0.0166148326 -0.0176304536
6
i = 6, time = 3.000, E = -34.3284123938
O 0.0281662678 -0.0046881479 0.0148296955
O 0.0060040547 -0.0146480193 -0.0040490901
H 0.0108475167 -0.0051588873 0.0044067330
H -0.0408814111 0.0095038932 -0.0166358603
H -0.0090712790 0.0095284617 0.0056498749
H 0.0020807572 0.0046966693 -0.0023430550
6
i = 9, time = 4.500, E = -34.3285982555
O 0.0012986124 0.0055958132 0.0080268729
O -0.0037946089 0.0215470472 -0.0028031321
H 0.0202015298 -0.0144688984 -0.0006764244
H -0.0224236823 0.0088983437 -0.0046822398
H 0.0178766967 -0.0138368861 -0.0111595296
H -0.0149760490 -0.0087128434 0.0128179743
6
i = 10, time = 5.000, E = -34.3282870379
O -0.0113686409 0.0076384898 0.0006427492
O -0.0055062210 0.0286073756 -0.0018076711
H 0.0202130994 -0.0147546410 -0.0010870336
H -0.0091230759 0.0072344012 0.0031139494
H 0.0227426182 -0.0183175217 -0.0146901267
H -0.0178560776 -0.0112779270 0.0153524783
regtests/cp2k_2.6.2/md/print_settings/H2O-32-pos-1.xyz 0 → 100644
View file @ 4961e40b
6
i = 0, time = 0.000, E = -34.3303964710
O 2.2803980000 9.1465390000 5.0886960000
O 1.2517030000 2.4062610000 7.7699080000
H 1.7620190000 9.8204290000 5.5284540000
H 3.0959870000 9.1070880000 5.5881860000
H 0.5541290000 2.9826340000 8.0820240000
H 1.7712570000 2.9547790000 7.1821810000
6
i = 3, time = 1.500, E = -34.3279989781
O 2.2816569948 9.1463220223 5.0875919643
O 1.2464808250 2.4089259514 7.7679581102
H 1.7376017910 9.8176768475 5.5110703534
H 3.1398366791 9.0773366634 5.6100676793
H 0.5816795339 2.9798971014 8.0968435085
H 1.7872918494 2.9513202206 7.2111353246
6
i = 6, time = 3.000, E = -34.3284123938
O 2.2848116168 9.1451387997 5.0866494510
O 1.2420611951 2.4088940254 7.7660011551
H 1.7090732160 9.8245375564 5.5052476019
H 3.1557721856 9.0533599447 5.6206772705
H 0.5788535575 3.0026992793 8.1272265032
H 1.8213326965 2.9646247282 7.2224917951
6
i = 9, time = 4.500, E = -34.3285982555
O 2.2898069785 9.1436252146 5.0866444773
O 1.2380505706 2.4078718032 7.7637918013
H 1.6920290647 9.8261894866 5.5044715741
H 3.1289538455 9.0395163855 5.6142598682
H 0.5662695747 3.0355160242 8.1632992842
H 1.8577079508 2.9830741256 7.2311516146
6
i = 10, time = 5.000, E = -34.3282870379
O 2.2916014875 9.1431763260 5.0868100688
O 1.2366834078 2.4077552776 7.7630044423
H 1.6909790671 9.8235337924 5.5042564094
H 3.1130341664 9.0372111810 5.6100739746
H 0.5652070478 3.0441761067 8.1734257299
H 1.8669280879 2.9877213524 7.2364955946
regtests/cp2k_2.6.2/md/print_settings/H2O-32-vel-1.xyz 0 → 100644
View file @ 4961e40b
6
i = 0, time = 0.000, E = -34.3303964710
O 0.0000299284 0.0000082360 -0.0000216368
O -0.0001665963 0.0001143863 -0.0000622640
H -0.0005732926 -0.0003112611 -0.0007149779
H 0.0013083605 -0.0009262219 0.0006258560
H 0.0012002313 -0.0003701042 0.0002810523
H 0.0002340810 -0.0003388418 0.0011398583
6
i = 3, time = 1.500, E = -34.3279989781
O 0.0000621568 -0.0000228735 -0.0000367647
O -0.0001473763 0.0000386669 -0.0000579038
H -0.0008685849 0.0001182914 -0.0003346940
H 0.0010596831 -0.0008456506 0.0005633905
H 0.0003617154 0.0003083317 0.0006884934
H 0.0007905658 0.0001699508 0.0005825225
6
i = 6, time = 3.000, E = -34.3284123938
O 0.0001292006 -0.0000447573 -0.0000155271
O -0.0001250624 -0.0000282456 -0.0000631128
H -0.0007644774 0.0001977514 -0.0000665600
H -0.0001786192 -0.0005869829 0.0000473549
H -0.0003829438 0.0009687598 0.0010934476
H 0.0011720378 0.0005579199 0.0002160526
6
i = 9, time = 4.500, E = -34.3285982555
O 0.0001635949 -0.0000430207 0.0000122940
O -0.0001236421 -0.0000182885 -0.0000709875
H -0.0002096270 -0.0001613961 -0.0000158655
H -0.0013292509 -0.0002607972 -0.0003563387
H -0.0001976950 0.0008695436 0.0009885390
H 0.0009271520 0.0004738628 0.0004164474
6
i = 10, time = 5.000, E = -34.3282870379
O 0.0001600263 -0.0000383308 0.0000153662
O -0.0001269381 -0.0000005151 -0.0000726214
H 0.0000177093 -0.0003257814 -0.0000257852
H -0.0015067045 -0.0001700489 -0.0003651605
H 0.0000307926 0.0006886719 0.0008431321
H 0.0007424681 0.0003614127 0.0005749089
regtests/cp2k_2.6.2/md/print_settings/H2O-32.inp 0 → 100644
View file @ 4961e40b
&FORCE_EVAL
METHOD QS
STRESS_TENSOR ANALYTICAL
&DFT
BASIS_SET_FILE_NAME ../../BASIS_SET
POTENTIAL_FILE_NAME ../../GTH_POTENTIALS
&MGRID
CUTOFF 200
REL_CUTOFF 30
&END MGRID
&QS
EPS_DEFAULT 1.0E-12
WF_INTERPOLATION PS
EXTRAPOLATION_ORDER 3
&END QS
&SCF
SCF_GUESS ATOMIC
&PRINT
&RESTART OFF
&END
&END
&END SCF
&XC
&XC_FUNCTIONAL Pade
&END XC_FUNCTIONAL
&END XC
&END DFT
&SUBSYS
&CELL
ABC 9.8528 9.8528 9.8528
&END CELL
&COORD
O 2.280398 9.146539 5.088696
O 1.251703 2.406261 7.769908
H 1.762019 9.820429 5.528454
H 3.095987 9.107088 5.588186
H 0.554129 2.982634 8.082024
H 1.771257 2.954779 7.182181
&END COORD
&KIND H
BASIS_SET DZVP-GTH-PADE
POTENTIAL GTH-PADE-q1
&END KIND
&KIND O
BASIS_SET DZVP-GTH-PADE
POTENTIAL GTH-PADE-q6
&END KIND
&END SUBSYS
&END FORCE_EVAL
&GLOBAL
PROJECT H2O-32
RUN_TYPE MD
PRINT_LEVEL MEDIUM
&END GLOBAL
&MOTION
&MD
ENSEMBLE NVE
STEPS 10
TIMESTEP 0.5
TEMPERATURE 300.0
&PRINT
&ENERGY
&EACH
MD 3
&END EACH
&END ENERGY
&END PRINT
&END MD
&PRINT
&CELL MEDIUM
&END CELL
&VELOCITIES
ADD_LAST NUMERIC
&EACH
MD 3
&END EACH
&END VELOCITIES
&FORCES
ADD_LAST NUMERIC
&EACH
MD 3
&END EACH
&END FORCES
&STRESS MEDIUM
&END STRESS