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Commit e82b9773 authored by Lauri Himanen's avatar Lauri Himanen
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Added the parsing of periodicity and XC functional. XC functional parsing... 

Added the parsing of periodicity and XC functional. XC functional parsing still needs some work, but the most common ones work.
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parser/parser-cpmd/cpmdparser/versions/cpmd41/commonparser.py
+ 3
− 0
View file @ e82b9773
...@@ -209,6 +209,9 @@ class CPMDCommonParser(CommonParser): ...@@ -209,6 +209,9 @@ class CPMDCommonParser(CommonParser):
backend.addValue("program_name", "CPMD") backend.addValue("program_name", "CPMD")
backend.addValue("program_basis_set_type", "plane waves") backend.addValue("program_basis_set_type", "plane waves")
def onClose_section_system(self, backend, gIndex, section):
self.cache_service.addArrayValues("configuration_periodic_dimensions")
def onClose_section_method(self, backend, gIndex, section): def onClose_section_method(self, backend, gIndex, section):
backend.addValue("electronic_structure_method", "DFT") backend.addValue("electronic_structure_method", "DFT")
basis_id = backend.openSection("section_method_basis_set") basis_id = backend.openSection("section_method_basis_set")
......
parser/parser-cpmd/cpmdparser/versions/cpmd41/inputparser.py
+ 139
− 1
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import os import os
import pickle import pickle
import logging import logging
import numpy as np
from nomadcore.baseclasses import BasicParser from nomadcore.baseclasses import BasicParser
from cpmdparser.generic.inputparsing import metainfo_data_prefix, metainfo_section_prefix from cpmdparser.generic.inputparsing import metainfo_data_prefix, metainfo_section_prefix
logger = logging.getLogger("nomad") logger = logging.getLogger("nomad")
...@@ -18,6 +19,7 @@ class CPMDInputParser(BasicParser): ...@@ -18,6 +19,7 @@ class CPMDInputParser(BasicParser):
self.cache_service.add("trajectory_range", False) self.cache_service.add("trajectory_range", False)
self.cache_service.add("trajectory_sample", False) self.cache_service.add("trajectory_sample", False)
self.cache_service.add("print_freq", 1) self.cache_service.add("print_freq", 1)
self.cache_service.add("configuration_periodic_dimensions", single=False, update=False)
def parse(self): def parse(self):
self.setup_input_tree(self.parser_context.version_id) self.setup_input_tree(self.parser_context.version_id)
...@@ -104,7 +106,10 @@ class CPMDInputParser(BasicParser): ...@@ -104,7 +106,10 @@ class CPMDInputParser(BasicParser):
old_keyword_object.parameters = "\n".join(parameters) old_keyword_object.parameters = "\n".join(parameters)
parameters = [] parameters = []
options = splitted[i_match+1:] options = splitted[i_match+1:]
if options:
options = " ".join(options) options = " ".join(options)
else:
options = None
keyword_object.options = options keyword_object.options = options
keyword_object.accessed = True keyword_object.accessed = True
old_keyword_object = keyword_object old_keyword_object = keyword_object
...@@ -114,6 +119,7 @@ class CPMDInputParser(BasicParser): ...@@ -114,6 +119,7 @@ class CPMDInputParser(BasicParser):
parameters.append(line) parameters.append(line)
def analyze_input(self): def analyze_input(self):
# Get the trajectory print settings # Get the trajectory print settings
root = self.input_tree root = self.input_tree
cpmd = root.get_section("CPMD") cpmd = root.get_section("CPMD")
...@@ -134,6 +140,138 @@ class CPMDInputParser(BasicParser): ...@@ -134,6 +140,138 @@ class CPMDInputParser(BasicParser):
else: else:
self.cache_service["print_freq"] = print_freq self.cache_service["print_freq"] = print_freq
# Get the periodicity settings
system = root.get_section("SYSTEM")
symmetry = system.get_keyword("SYMMETRY")
symmetry_parameters = symmetry.parameters.strip()
cluster = system.get_keyword("CLUSTER")
surface = system.get_keyword("SURFACE")
polymer = system.get_keyword("POLYMER")
# Bulk
if symmetry_parameters != "0" and symmetry_parameters != "ISOLATED" and cluster.accessed is False:
periodicity = [True, True, True]
# Surface
elif surface.accessed:
options = surface.options
if options is None:
options = "XY"
else:
options = options.strip()
if options == "XY":
periodicity = [True, True, False]
elif options == "XZ":
periodicity = [True, False, True]
elif options == "YZ":
periodicity = [False, True, True]
# Polymer
elif polymer.accessed:
periodicity = [True, False, False]
# Isolated
elif cluster.accessed or symmetry_parameters == "ISOLATED" or symmetry_parameters == "0":
periodicity = [False, False, False]
self.cache_service["configuration_periodic_dimensions"] = np.array(periodicity)
# Get the XC functional
class XCFunctional(object):
def __init__(self, name, weight=1, parameters=None):
self.name = name
self.weight = weight
self.parameters = parameters
xc_list = []
dft = root.get_section("DFT")
if dft is not None:
functional = dft.get_keyword("FUNCTIONAL")
if functional is not None:
xc = functional.options
if xc is not None:
xc = xc.strip()
if xc == "LDA":
xc_list.append(XCFunctional("LDA_XC_TETER93"))
elif xc == "BLYP":
xc_list.append(XCFunctional("GGA_X_B88"))
xc_list.append(XCFunctional("GGA_C_LYP"))
elif xc == "B3LYP":
xc_list.append(XCFunctional("HYB_GGA_XC_B3LYP"))
elif xc == "PBE":
xc_list.append(XCFunctional("GGA_X_PBE"))
xc_list.append(XCFunctional("GGA_C_PBE"))
elif xc == "OLYP":
xc_list.append(XCFunctional("GGA_X_OPTX"))
xc_list.append(XCFunctional("GGA_C_LYP"))
elif xc == "HCTH":
xc_list.append(XCFunctional("GGA_XC_HCTH_120"))
elif xc == "PBE0":
xc_list.append(XCFunctional("HYB_GGA_XC_PBEH"))
elif xc == "BP":
xc_list.append(XCFunctional("GGA_X_B88"))
xc_list.append(XCFunctional("GGA_C_P86"))
elif xc == "XLYP":
xc_list.append(XCFunctional("GGA_XC_XLYP"))
elif xc == "PBES":
xc_list.append(XCFunctional("GGA_C_PBE_SOL"))
xc_list.append(XCFunctional("GGA_X_PBE_SOL"))
elif xc == "REVPBE":
xc_list.append(XCFunctional("GGA_C_PBE"))
xc_list.append(XCFunctional("GGA_X_PBE_R"))
elif xc == "TPSS":
xc_list.append(XCFunctional("MGGA_C_TPSS"))
xc_list.append(XCFunctional("MGGA_X_TPSS"))
# This version of OPTX is not yet found on the official list
# elif xc == "OPTX":
elif xc == "B1LYP":
xc_list.append(XCFunctional("HYB_GGA_XC_B1LYP"))
elif xc == "X3LYP":
xc_list.append(XCFunctional("HYB_GGA_XC_X3LYP"))
elif xc == "HSE06":
xc_list.append(XCFunctional("HYB_GGA_XC_HSE06"))
# Sort the functionals alphabetically by name
xc_list.sort(key=lambda x: x.name)
xc_summary = ""
# For every defined functional, stream the information to the
# backend and construct the summary string
for i, functional in enumerate(xc_list):
gId = self.backend.openSection("section_XC_functionals")
self.backend.addValue("XC_functional_name", functional.name)
self.backend.addValue("XC_functional_weight", functional.weight)
if functional.parameters is not None:
pass
self.backend.closeSection("section_XC_functionals", gId)
if i != 0:
xc_summary += "+"
xc_summary += "{}*{}".format(functional.weight, functional.name)
if functional.parameters is not None:
xc_summary += ":{}".format()
# Stream summary
if xc_summary is not "":
self.backend.addValue("XC_functional", xc_summary)
def fill_metadata(self): def fill_metadata(self):
"""Goes through the input data and pushes everything to the """Goes through the input data and pushes everything to the
backend. backend.
......
test/unittests/cpmd_4.1/periodicity/bulk/GEOMETRY 0 → 100644
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8.259992891426 7.558904499132 7.558904499132 0.017798524379 -0.000000000000 -0.000000000000
6.857816106837 7.558904499132 7.558904499132 -0.017798524379 -0.000000000000 -0.000000000000
test/unittests/cpmd_4.1/periodicity/bulk/GEOMETRY.xyz 0 → 100644
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2
GEOMETRY FILE / created by CPMD
H 4.371000000000 4.000000000000 4.000000000000 0.009418573488 -0.000000000000 -0.000000000000
H 3.629000000000 4.000000000000 4.000000000000 -0.009418573488 -0.000000000000 -0.000000000000
test/unittests/cpmd_4.1/periodicity/bulk/LATEST 0 → 100644
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./RESTART.1
1
test/unittests/cpmd_4.1/periodicity/bulk/RESTART.1 0 → 100644
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File added
test/unittests/cpmd_4.1/periodicity/bulk/input.inp 0 → 100755
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&INFO
isolated hydrogen molecule.
single point calculation.
&END
&CPMD
OPTIMIZE WAVEFUNCTION
CONVERGENCE ORBITALS
1.0d-7
CENTER MOLECULE ON
PRINT FORCES ON
&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
test/unittests/cpmd_4.1/periodicity/bulk/output.out 0 → 100644
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cp_groups: we are using a 1 x 1 grid (groups x nprocs).
PROGRAM CPMD STARTED AT: 2016-07-29 10:11:26.819
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/periodicity/bulk
THE TEMPORARY DIRECTORY IS:
/home/lauri/Dropbox/nomad-dev/nomad-lab-base/parsers/cpmd/test/unittests/cpmd_4.1/periodicity/bulk
THE PROCESS ID IS: 6110
THE JOB WAS SUBMITTED BY: lauri
******************************************************************************
* INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO *
******************************************************************************
* isolated hydrogen molecule. *
* single point calculation. *
******************************************************************************
SINGLE POINT DENSITY OPTIMIZATION
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
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
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: 0.50 SECONDS
*** WFOPTS| 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
TIME FOR WAVEFUNCTION INITIALIZATION: 0.88 SECONDS
*** RWFOPT| SIZE OF THE PROGRAM IS NOT AVAILABLE ***
EWALD| SUM IN REAL SPACE OVER 1* 1* 1 CELLS
TOTAL INTEGRATED ELECTRONIC DENSITY
IN G-SPACE = 2.0000000000
IN R-SPACE = 2.0000000000
(K+E1+L+N+X) TOTAL ENERGY = -1.09689770 A.U.
(K) KINETIC ENERGY = 0.81247072 A.U.
(E1=A-S+R) ELECTROSTATIC ENERGY = -0.48640053 A.U.
(S) ESELF = 0.66490380 A.U.
(R) ESR = 0.17302593 A.U.
(L) LOCAL PSEUDOPOTENTIAL ENERGY = -0.84879440 A.U.
(N) N-L PSEUDOPOTENTIAL ENERGY = 0.00000000 A.U.
(X) EXCHANGE-CORRELATION ENERGY = -0.57417350 A.U.
NFI GEMAX CNORM ETOT DETOT TCPU
1 3.816E-02 2.886E-03 -1.096898 0.000E+00 0.25
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 0.27
4 6.115E-04 4.235E-05 -1.132456 -8.056E-05 0.28
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 0.25
7 6.288E-06 4.459E-07 -1.132460 -7.717E-09 0.25
8 7.941E-07 1.282E-07 -1.132460 -4.283E-10 0.23
9 1.237E-07 2.861E-08 -1.132460 -1.992E-11 0.22
10 2.278E-08 5.401E-09 -1.132460 -8.606E-13 0.23
RESTART INFORMATION WRITTEN ON FILE ./RESTART.1
*** RWFOPT| SIZE OF THE PROGRAM IS NOT AVAILABLE ***
****************************************************************
* *
* FINAL RESULTS *
* *
****************************************************************
ATOM COORDINATES GRADIENTS (-FORCES)
1 H 8.2600 7.5589 7.5589 1.780E-02 -1.104E-16 -9.425E-17
2 H 6.8578 7.5589 7.5589 -1.780E-02 -1.867E-16 -1.490E-16
****************************************************************
ELECTRONIC GRADIENT:
MAX. COMPONENT = 1.15980E-08 NORM = 1.11525E-09
NUCLEAR GRADIENT:
MAX. COMPONENT = 1.77985E-02 NORM = 1.02760E-02
TOTAL INTEGRATED ELECTRONIC DENSITY
IN G-SPACE = 2.0000000000
IN R-SPACE = 2.0000000000
(K+E1+L+N+X) TOTAL ENERGY = -1.13245953 A.U.
(K) KINETIC ENERGY = 1.09007149 A.U.
(E1=A-S+R) ELECTROSTATIC ENERGY = -0.47319176 A.U.
(S) ESELF = 0.66490380 A.U.
(R) ESR = 0.17302593 A.U.
(L) LOCAL PSEUDOPOTENTIAL ENERGY = -1.09902228 A.U.
(N) N-L PSEUDOPOTENTIAL ENERGY = 0.00000000 A.U.
(X) EXCHANGE-CORRELATION ENERGY = -0.65031699 A.U.
****************************************************************
****************************************************************
* *
* TIMING *
* *
****************************************************************
SUBROUTINE CALLS SELF TIME TOTAL TIME
AVERAGE MAXIMUM AVERAGE MAXIMUM
cpmd 1 0.01 0.01 3.98 3.98
rwfopt 1 0.00 0.00 3.48 3.48
updwf 11 0.00 0.00 2.60 2.60
forcedr 11 0.00 0.00 2.55 2.55
forces 11 0.00 0.00 2.55 2.55
forces_a 11 0.00 0.00 1.98 1.98
rscpot 11 0.00 0.00 1.98 1.98
vofrho 12 0.00 0.00 1.93 1.93
VOFRHOB 12 0.05 0.05 1.32 1.32
INVFFTN 37 1.22 1.22 1.22 1.22
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
FWFFTN 25 0.75 0.75 0.75 0.75
xcener_new 12 0.05 0.05 0.71 0.71
vpsi 13 0.07 0.07 0.69 0.69
mikeu 12 0.66 0.66 0.66 0.66
VOFRHOA 12 0.03 0.03 0.62 0.62
ATRHO 1 0.39 0.39 0.43 0.43
rhoofr 11 0.08 0.08 0.37 0.37
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
dist_ksmat 1 0.00 0.00 0.12 0.12
NUMPW 1 0.12 0.12 0.12 0.12
RINFORCE 1 0.00 0.00 0.10 0.10
loadpa_b 1 0.10 0.10 0.10 0.10
FORMFN 1 0.10 0.10 0.10 0.10
loadpa_c 1 0.09 0.09 0.09 0.09
ppener 12 0.07 0.07 0.07 0.07
loadpa_a 1 0.04 0.04 0.04 0.04
EICALC 12 0.04 0.04 0.04 0.04
odiis 11 0.04 0.04 0.04 0.04
PUTPS 1 0.01 0.01 0.01 0.01
potfor 1 0.01 0.01 0.01 0.01
fftprp 1 0.00 0.00 0.00 0.00
****************************************************************
CPU TIME : 0 HOURS 0 MINUTES 3.96 SECONDS
ELAPSED TIME : 0 HOURS 0 MINUTES 3.99 SECONDS
*** CPMD| SIZE OF THE PROGRAM IS NOT AVAILABLE ***
PROGRAM CPMD ENDED AT: 2016-07-29 10:11:30.805
test/unittests/cpmd_4.1/periodicity/bulk/run.sh 0 → 100755
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export CPMD_PP_LIBRARY_PATH=../../
export OMP_NUM_THREADS=1
cpmd41 input.inp > output.out
test/unittests/cpmd_4.1/periodicity/cluster/GEOMETRY 0 → 100644
+ 2
− 0
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8.259992891426 7.558904499132 7.558904499132 0.017803915410 -0.000000000000 -0.000000000000
6.857816106837 7.558904499132 7.558904499132 -0.017803915410 -0.000000000000 -0.000000000000
test/unittests/cpmd_4.1/periodicity/cluster/GEOMETRY.xyz 0 → 100644
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2
GEOMETRY FILE / created by CPMD
H 4.371000000000 4.000000000000 4.000000000000 0.009421426299 -0.000000000000 -0.000000000000
H 3.629000000000 4.000000000000 4.000000000000 -0.009421426299 -0.000000000000 -0.000000000000
test/unittests/cpmd_4.1/periodicity/cluster/LATEST 0 → 100644
+ 2
− 0
View file @ e82b9773
./RESTART.1
1
test/unittests/cpmd_4.1/periodicity/cluster/RESTART.1 0 → 100644
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− 0
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File added
test/unittests/cpmd_4.1/periodicity/cluster/input.inp 0 → 100755
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&INFO
isolated hydrogen molecule.
single point calculation.
&END
&CPMD
OPTIMIZE WAVEFUNCTION
CONVERGENCE ORBITALS
1.0d-7
CENTER MOLECULE ON
PRINT FORCES ON
&END
&SYSTEM
CLUSTER
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
test/unittests/cpmd_4.1/periodicity/cluster/output.out 0 → 100644
+ 291
− 0
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cp_groups: we are using a 1 x 1 grid (groups x nprocs).
PROGRAM CPMD STARTED AT: 2016-07-29 10:16:57.700
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/periodicity/cluster
THE TEMPORARY DIRECTORY IS:
/home/lauri/Dropbox/nomad-dev/nomad-lab-base/parsers/cpmd/test/unittests/cpmd_4.1/periodicity/cluster
THE PROCESS ID IS: 6722
THE JOB WAS SUBMITTED BY: lauri
******************************************************************************
* INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO *
******************************************************************************
* isolated hydrogen molecule. *
* single point calculation. *
******************************************************************************
SINGLE POINT DENSITY OPTIMIZATION
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
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
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 ***
>>>>>>>> CENTER OF MASS HAS BEEN MOVED TO CENTER OF BOX <<<<<<<<
***************************** 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 1 180
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 ***************************
THIS IS AN ISOLATED SYSTEM CALCULATION
POISSON EQUATION SOLVER : HOCKNEY
COULOMB SMOOTHING RADIUS : 1.080
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 ***
*** CLUSTER| SIZE OF THE PROGRAM IS NOT AVAILABLE ***
GENERATE ATOMIC BASIS SET
H SLATER ORBITALS
1S ALPHA= 1.0000 OCCUPATION= 1.00
INITIALIZATION TIME: 0.96 SECONDS
*** WFOPTS| 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
TIME FOR WAVEFUNCTION INITIALIZATION: 1.52 SECONDS
*** RWFOPT| SIZE OF THE PROGRAM IS NOT AVAILABLE ***
EWALD| SUM IN REAL SPACE OVER 1* 1* 1 CELLS
TOTAL INTEGRATED ELECTRONIC DENSITY
IN G-SPACE = 2.0000000000
IN R-SPACE = 2.0000000000
(K+E1+L+N+X) TOTAL ENERGY = -1.09689904 A.U.
(K) KINETIC ENERGY = 0.81247072 A.U.
(E1=A-S+R) ELECTROSTATIC ENERGY = -0.48640187 A.U.
(S) ESELF = 0.66490380 A.U.
(R) ESR = 0.17302593 A.U.
(L) LOCAL PSEUDOPOTENTIAL ENERGY = -0.84879440 A.U.
(N) N-L PSEUDOPOTENTIAL ENERGY = 0.00000000 A.U.
(X) EXCHANGE-CORRELATION ENERGY = -0.57417350 A.U.
NFI GEMAX CNORM ETOT DETOT TCPU
1 3.816E-02 2.886E-03 -1.096899 0.000E+00 0.89
2 8.628E-03 1.041E-03 -1.130806 -3.391E-02 0.83
3 2.735E-03 2.293E-04 -1.132378 -1.572E-03 0.92
4 6.127E-04 4.247E-05 -1.132458 -8.054E-05 0.90
5 1.532E-04 6.948E-06 -1.132462 -3.346E-06 0.82
6 3.884E-05 1.372E-06 -1.132462 -1.294E-07 0.80
7 6.248E-06 4.342E-07 -1.132462 -7.648E-09 0.79
8 7.827E-07 1.288E-07 -1.132462 -4.005E-10 0.80
9 1.374E-07 2.900E-08 -1.132462 -2.031E-11 0.79
10 1.599E-08 5.075E-09 -1.132462 -9.228E-13 0.80
RESTART INFORMATION WRITTEN ON FILE ./RESTART.1
*** RWFOPT| SIZE OF THE PROGRAM IS NOT AVAILABLE ***
****************************************************************
* *
* FINAL RESULTS *
* *
****************************************************************
ATOM COORDINATES GRADIENTS (-FORCES)
1 H 8.2600 7.5589 7.5589 1.780E-02 -7.864E-17 -1.082E-16
2 H 6.8578 7.5589 7.5589 -1.780E-02 -1.689E-16 -1.551E-16
****************************************************************
ELECTRONIC GRADIENT:
MAX. COMPONENT = 5.93705E-09 NORM = 9.63321E-10
NUCLEAR GRADIENT:
MAX. COMPONENT = 1.78039E-02 NORM = 1.02791E-02
TOTAL INTEGRATED ELECTRONIC DENSITY
IN G-SPACE = 2.0000000000
IN R-SPACE = 2.0000000000
(K+E1+L+N+X) TOTAL ENERGY = -1.13246180 A.U.
(K) KINETIC ENERGY = 1.09007002 A.U.
(E1=A-S+R) ELECTROSTATIC ENERGY = -0.47319328 A.U.
(S) ESELF = 0.66490380 A.U.
(R) ESR = 0.17302593 A.U.
(L) LOCAL PSEUDOPOTENTIAL ENERGY = -1.09902099 A.U.
(N) N-L PSEUDOPOTENTIAL ENERGY = 0.00000000 A.U.
(X) EXCHANGE-CORRELATION ENERGY = -0.65031755 A.U.
****************************************************************
****************************************************************
* *
* TIMING *
* *
****************************************************************
SUBROUTINE CALLS SELF TIME TOTAL TIME
AVERAGE MAXIMUM AVERAGE MAXIMUM
cpmd 1 0.01 0.01 11.47 11.47
rwfopt 1 0.01 0.01 10.51 10.51
updwf 11 0.00 0.00 8.99 8.99
forcedr 11 0.00 0.00 8.95 8.95
forces 11 0.00 0.00 8.95 8.95
vofrho 12 0.00 0.00 8.87 8.87
forces_a 11 0.00 0.00 8.32 8.32
rscpot 11 0.00 0.00 8.32 8.32
VOFRHOH 12 0.13 0.13 7.51 7.51
HIP 12 5.88 5.88 5.88 5.88
INVFFTN 49 1.78 1.78 1.78 1.78
initrun 1 0.00 0.00 1.51 1.51
rinitwf 1 0.00 0.00 1.51 1.51
ATOMWF 1 0.00 0.00 1.51 1.51
VOFRHOB 12 0.11 0.11 1.35 1.35
FWFFTN 37 1.19 1.19 1.19 1.19
vpsi 13 0.12 0.12 0.75 0.75
xcener_new 12 0.06 0.06 0.69 0.69
mikeu 12 0.64 0.64 0.64 0.64
initclust 1 0.01 0.01 0.48 0.48
HOCKNEY 1 0.47 0.47 0.47 0.47
rhoofr 11 0.13 0.13 0.42 0.42
ATRHO 1 0.38 0.38 0.42 0.42
rinit 1 0.00 0.00 0.26 0.26
rggen 1 0.01 0.01 0.26 0.26
loadpa 1 0.01 0.01 0.25 0.25
dist_ksmat 1 0.00 0.00 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
loadpa_c 1 0.09 0.09 0.09 0.09
loadpa_a 1 0.04 0.04 0.04 0.04
EICALC 12 0.04 0.04 0.04 0.04
odiis 11 0.04 0.04 0.04 0.04
****************************************************************
CPU TIME : 0 HOURS 0 MINUTES 11.47 SECONDS
ELAPSED TIME : 0 HOURS 0 MINUTES 11.47 SECONDS
*** CPMD| SIZE OF THE PROGRAM IS NOT AVAILABLE ***
PROGRAM CPMD ENDED AT: 2016-07-29 10:17:09.168
test/unittests/cpmd_4.1/periodicity/cluster/run.sh 0 → 100755
+ 3
− 0
View file @ e82b9773
export CPMD_PP_LIBRARY_PATH=../../
export OMP_NUM_THREADS=1
cpmd41 input.inp > output.out
test/unittests/cpmd_4.1/periodicity/isolated/GEOMETRY 0 → 100644
+ 2
− 0
View file @ e82b9773
8.259992891426 7.558904499132 7.558904499132 0.017803915410 -0.000000000000 -0.000000000000
6.857816106837 7.558904499132 7.558904499132 -0.017803915410 -0.000000000000 -0.000000000000
test/unittests/cpmd_4.1/periodicity/isolated/GEOMETRY.xyz 0 → 100644
+ 4
− 0
View file @ e82b9773
2
GEOMETRY FILE / created by CPMD
H 4.371000000000 4.000000000000 4.000000000000 0.009421426299 -0.000000000000 -0.000000000000
H 3.629000000000 4.000000000000 4.000000000000 -0.009421426299 -0.000000000000 -0.000000000000
test/unittests/cpmd_4.1/periodicity/isolated/LATEST 0 → 100644
+ 2
− 0
View file @ e82b9773
./RESTART.1
1
test/unittests/cpmd_4.1/periodicity/isolated/RESTART.1 0 → 100644
+ 0
− 0
View file @ e82b9773
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