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Commit 2c552833 authored by speckhard's avatar speckhard
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Added parser test data and added Matid package.

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.gitignore
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......@@ -15,3 +15,4 @@ test_*
local/
target/
*.swp
*.vscode
requirements-dep.txt
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......@@ -7,6 +7,7 @@ future
enum34
scipy
spglib
matid
ase==3.15.0
systax==0.1.2
Pint==0.7.2
......
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cp_groups: we are using a 1 x 1 grid (groups x nprocs).
PROGRAM CPMD STARTED AT: 2016-07-04 14:05:06.851
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/h2
THE TEMPORARY DIRECTORY IS:
/home/lauri/Dropbox/nomad-dev/nomad-lab-base/parsers/cpmd/test/unittests/cpmd_4.1/h2
THE PROCESS ID IS: 32589
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: 0.48 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: 0.83 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 0.23
2 8.628E-03 1.041E-03 -1.130803 -3.391E-02 0.22
3 2.736E-03 2.293E-04 -1.132376 -1.572E-03 0.22
4 6.115E-04 4.235E-05 -1.132456 -8.056E-05 0.22
5 1.532E-04 7.007E-06 -1.132459 -3.315E-06 0.24
6 3.895E-05 1.396E-06 -1.132460 -1.338E-07 0.22
7 6.288E-06 4.459E-07 -1.132460 -7.717E-09 0.22
8 7.941E-07 1.282E-07 -1.132460 -4.283E-10 0.22
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 0.22
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 0.00 0.00 3.67 3.67
rwfopt 1 0.00 0.00 3.20 3.20
updwf 11 0.00 0.00 2.37 2.37
forcedr 11 0.00 0.00 2.33 2.33
forces 11 0.00 0.00 2.33 2.33
forces_a 11 0.00 0.00 1.80 1.80
rscpot 11 0.00 0.00 1.80 1.80
vofrho 12 0.00 0.00 1.79 1.79
VOFRHOB 12 0.04 0.04 1.22 1.22
INVFFTN 37 1.12 1.12 1.12 1.12
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
FWFFTN 25 0.69 0.69 0.69 0.69
xcener_new 12 0.04 0.04 0.67 0.67
mikeu 12 0.63 0.63 0.63 0.63
vpsi 13 0.06 0.06 0.63 0.63
VOFRHOA 12 0.03 0.03 0.57 0.57
ATRHO 1 0.35 0.35 0.39 0.39
rhoofr 11 0.07 0.07 0.34 0.34
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 0.11 0.11
RINFORCE 1 0.00 0.00 0.10 0.10
NUMPW 1 0.10 0.10 0.10 0.10
loadpa_b 1 0.10 0.10 0.10 0.10
loadpa_c 1 0.10 0.10 0.10 0.10
FORMFN 1 0.10 0.10 0.10 0.10
ppener 12 0.06 0.06 0.06 0.06
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
forces_b 11 0.00 0.00 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 3.67 SECONDS
ELAPSED TIME : 0 HOURS 0 MINUTES 3.67 SECONDS
*** CPMD| SIZE OF THE PROGRAM IS NOT AVAILABLE ***
PROGRAM CPMD ENDED AT: 2016-07-04 14:05:10.523
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TEST11 - MGO BULK
CRYSTAL
0 0 0
225
4.21
2
12 0. 0. 0.
8 0.5 0.5 0.5
END
12 3
0 0 8 2. 1.
68371.875 0.0002226
9699.34009 0.0018982
2041.176786 0.0110451
529.862906 0.0500627
159.186000 0.169123
54.6848 0.367031
21.2357 0.400410
8.74604 0.14987
0 1 6 8. 1.
156.795 -0.00624 0.00772
31.0339 -0.07882 0.06427
9.6453 -0.07992 0.2104
3.7109 0.29063 0.34314
1.61164 0.57164 0.3735
0.64294 0.30664 0.23286
0 1 1 0. 1.
0.4 1. 1.
8 3
0 0 8 2. 1.
4000. 0.00144
1355.58 0.00764
248.545 0.05370
69.5339 0.16818
23.8868 0.36039
9.27593 0.38612
3.82034 0.14712
1.23514 0.07105
0 1 5 8. 1.
52.1878 -0.00873 0.00922
10.3293 -0.08979 0.07068
3.21034 -0.04079 0.20433
1.23514 0.37666 0.34958
0.536420 0.42248 0.27774
0 1 1 0. 1.
0.210000 1. 1.
99 0
END
SHRINK
8 8
FMIXING
30
PPAN
END
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argument 1 = input.nw
============================== echo of input deck ==============================
start qmd_dft_h2o_svr
echo
print low
geometry noautosym noautoz
O 0.00000000 -0.01681748 0.11334792
H 0.00000000 0.81325914 -0.34310308
H 0.00000000 -0.67863597 -0.56441201
end
basis
* library 6-31G*
end
dft
xc pbe0
end
qmd
nstep_nucl 5
dt_nucl 10.0
targ_temp 200.0
com_step 10
thermostat svr 100.0
print_xyz 5
end
task dft qmd
================================================================================
Northwest Computational Chemistry Package (NWChem) 6.6
------------------------------------------------------
Environmental Molecular Sciences Laboratory
Pacific Northwest National Laboratory
Richland, WA 99352
Copyright (c) 1994-2015
Pacific Northwest National Laboratory
Battelle Memorial Institute
NWChem is an open-source computational chemistry package
distributed under the terms of the
Educational Community License (ECL) 2.0
A copy of the license is included with this distribution
in the LICENSE.TXT file
ACKNOWLEDGMENT
--------------
This software and its documentation were developed at the
EMSL at Pacific Northwest National Laboratory, a multiprogram
national laboratory, operated for the U.S. Department of Energy
by Battelle under Contract Number DE-AC05-76RL01830. Support
for this work was provided by the Department of Energy Office
of Biological and Environmental Research, Office of Basic
Energy Sciences, and the Office of Advanced Scientific Computing.
Job information
---------------
hostname = lenovo700
program = nwchem
date = Wed Sep 14 15:04:49 2016
compiled = Mon_Feb_15_08:24:17_2016
source = /build/nwchem-MF0R1k/nwchem-6.6+r27746
nwchem branch = 6.6
nwchem revision = 27746
ga revision = 10594
input = input.nw
prefix = qmd_dft_h2o_svr.
data base = ./qmd_dft_h2o_svr.db
status = startup
nproc = 1
time left = -1s
Memory information
------------------
heap = 13107198 doubles = 100.0 Mbytes
stack = 13107195 doubles = 100.0 Mbytes
global = 26214400 doubles = 200.0 Mbytes (distinct from heap & stack)
total = 52428793 doubles = 400.0 Mbytes
verify = yes
hardfail = no
Directory information
---------------------
0 permanent = .
0 scratch = .
NWChem Input Module
-------------------
Scaling coordinates for geometry "geometry" by 1.889725989
(inverse scale = 0.529177249)
Geometry "geometry" -> ""
-------------------------
Output coordinates in angstroms (scale by 1.889725989 to convert to a.u.)
No. Tag Charge X Y Z
---- ---------------- ---------- -------------- -------------- --------------
1 O 8.0000 0.00000000 -0.01682581 0.11342109
2 H 1.0000 0.00000000 0.81325081 -0.34302991
3 H 1.0000 0.00000000 -0.67864430 -0.56433884
Atomic Mass
-----------
O 15.994910
H 1.007825
Effective nuclear repulsion energy (a.u.) 9.2887672039
Nuclear Dipole moment (a.u.)
----------------------------
X Y Z
---------------- ---------------- ----------------
0.0000000000 0.0000000000 0.0000000000
XYZ format geometry
-------------------
3
geometry
O 0.00000000 -0.01682581 0.11342109
H 0.00000000 0.81325081 -0.34302991
H 0.00000000 -0.67864430 -0.56433884
==============================================================================
internuclear distances
------------------------------------------------------------------------------
center one | center two | atomic units | angstroms
------------------------------------------------------------------------------
2 H | 1 O | 1.79013 | 0.94730
3 H | 1 O | 1.79012 | 0.94729
------------------------------------------------------------------------------
number of included internuclear distances: 2
==============================================================================
==============================================================================
internuclear angles
------------------------------------------------------------------------------
center 1 | center 2 | center 3 | degrees
------------------------------------------------------------------------------
2 H | 1 O | 3 H | 105.51
------------------------------------------------------------------------------
number of included internuclear angles: 1
==============================================================================
library name resolved from: .nwchemrc
library file name is: </home/lauri/nwchem-6.6/src/basis/libraries/>
Summary of "ao basis" -> "" (cartesian)
------------------------------------------------------------------------------
Tag Description Shells Functions and Types
---------------- ------------------------------ ------ ---------------------
* 6-31G* on all atoms
calling qmd_driver
NWChem QMD Module
-----------------
QMD Run Parameters
------------------
No. of nuclear steps: 5
Nuclear time step: 10.00
Target temp. (K): 200.00
Thermostat: svr
Tau: 100.00
Random seed: -8677
Nuclear integrator: velocity-verlet
No restart file found
Beginning with random velocities
Current temp. (K): 830.59
NWChem DFT Module
-----------------
Basis "ao basis" -> "ao basis" (cartesian)
-----
O (Oxygen)
----------
Exponent Coefficients
-------------- ---------------------------------------------------------
1 S 5.48467170E+03 0.001831
1 S 8.25234950E+02 0.013950
1 S 1.88046960E+02 0.068445
1 S 5.29645000E+01 0.232714
1 S 1.68975700E+01 0.470193
1 S 5.79963530E+00 0.358521
2 S 1.55396160E+01 -0.110778
2 S 3.59993360E+00 -0.148026
2 S 1.01376180E+00 1.130767
3 P 1.55396160E+01 0.070874
3 P 3.59993360E+00 0.339753
3 P 1.01376180E+00 0.727159
4 S 2.70005800E-01 1.000000
5 P 2.70005800E-01 1.000000
6 D 8.00000000E-01 1.000000
H (Hydrogen)
------------
Exponent Coefficients
-------------- ---------------------------------------------------------
1 S 1.87311370E+01 0.033495
1 S 2.82539370E+00 0.234727
1 S 6.40121700E-01 0.813757
2 S 1.61277800E-01 1.000000
Summary of "ao basis" -> "ao basis" (cartesian)
------------------------------------------------------------------------------
Tag Description Shells Functions and Types
---------------- ------------------------------ ------ ---------------------
O 6-31G* 6 15 3s2p1d
H 6-31G* 2 2 2s
Caching 1-el integrals