[CP2K-user] [CP2K:16651] maintaining space group
Pierre-André Cazade
pierre.andre.cazade at gmail.com
Tue Mar 1 09:31:56 UTC 2022
Hi Mozhreh,
If you look in the output file there is a section called SPGR| this is the
details about the space group. Here the correct space group was not
identified probably because your input geometry is not accurate enough.
-------------------------------------------------------------------------------
---- SPACE GROUP SYMMETRY INFORMATION
----
-------------------------------------------------------------------------------
SPGR| SPACE GROUP NUMBER:
1
SPGR| INTERNATIONAL SYMBOL:
P1
SPGR| POINT GROUP SYMBOL:
1
SPGR| SCHOENFLIES SYMBOL:
C1^1
SPGR| NUMBER OF SYMMETRY OPERATIONS:
1
SPGR| NUMBER OF UNIQUE ROTATIONS:
1
SPGR| NUMBER OF REDUCED SYMMETRY OPERATIONS:
1
SPGR| NUMBER OF PARTICLES AND SYMMETRIZED PARTICLES: 40
40
SPGR| NUMBER OF ATOMS AND SYMMETRIZED ATOMS: 40
40
SPGR| NUMBER OF CORES AND SYMMETRIZED CORES: 0
0
SPGR| NUMBER OF SHELLS AND SYMMETRIZED SHELLS: 0
0
Ideally, you would use a CIF file and the software VESTA to generate
accurate input coordinates. You can also try the keyword EPS_SYMMETRY to
make the identification of the space group more permissive. The default is
1e-4, try 1e-3 and make sure you get the correct space group in the output
file.
Regarding the trajectory file, I don't understand what you mean by cubic,
again in the output file the system stays monoclinic throughout the
optimization. You should have a restart file which is the one you want to
check regarding your final structure.
Finally, if your goal is a phonon analysis, you may want to use PHONOPY
which is compatible with CP2K, instead of the internal vibrational analysis.
Regards,
Pierre
On Tue, Mar 1, 2022 at 9:14 AM Mozhdeh Mohammadpour <
mozhdehmohammadpour at gmail.com> wrote:
> Hi Pierre,
>
> Please find attached.
>
>
> On Tuesday, March 1, 2022 at 9:11:46 AM UTC pierre.an... at gmail.com wrote:
>
>> Hi Mozhdeh,
>>
>> Could you please attach your output file and the last restart geometry?
>>
>> Regards,
>> Pierre
>>
>> On Tue, Mar 1, 2022 at 9:06 AM Mozhdeh Mohammadpour <
>> mozhdehmo... at gmail.com> wrote:
>>
>>> Dear CP2K expert,
>>>
>>> I am using the PBE method for the CELL optimization of a crystal
>>> with MONOCLINIC symmetry.
>>> Although I use KEEP_SPACE_GROUP true, KEEP_SYMMETRY true, the
>>> coordinates in the trajectory file are cubic (alpha_beta_gamma=90). I have
>>> to use final coordinates with correct symmetry for VIBRATIONAL_ANALYSIS.
>>>
>>> Here is my input:
>>> ***************************************************************
>>> &GLOBAL
>>> RUN_TYPE cell_opt
>>> PROJECT_NAME alpha-pbe-cell
>>> PRINT_LEVEL MEDIUM
>>> &END GLOBAL
>>> &FORCE_EVAL
>>> METHOD QUICKSTEP
>>> STRESS_TENSOR ANALYTICAL
>>> &DFT
>>> BASIS_SET_FILE_NAME BASIS_SET
>>> POTENTIAL_FILE_NAME POTENTIAL
>>> &POISSON
>>> PERIODIC XYZ
>>> POISSON_SOLVER PERIODIC
>>> &END POISSON
>>>
>>> &XC
>>> &XC_FUNCTIONAL PBE
>>> &END XC_FUNCTIONAL
>>> &XC_GRID
>>> ! defaults
>>> XC_SMOOTH_RHO NONE
>>> XC_DERIV PW
>>> &END XC_GRID
>>> &END XC
>>> CHARGE 0
>>> MULTIPLICITY 1
>>> &QS
>>> METHOD GPW
>>> EXTRAPOLATION USE_GUESS ! required for K-Point sampling
>>> &END QS
>>> &SCF
>>> SCF_GUESS atomic
>>> MAX_SCF 500
>>> &END SCF
>>>
>>> &MGRID
>>> NGRIDS 6
>>> CUTOFF 700
>>> REL_CUTOFF 60
>>> &END MGRID
>>> &PRINT
>>> &END PRINT
>>> &KPOINTS
>>> SCHEME MONKHORST-PACK 2 1 2
>>> WAVEFUNCTIONS complex
>>> FULL_GRID .TRUE.
>>> VERBOSE true
>>> UNITS CART_ANGSTROM
>>> &END KPOINTS
>>> &END DFT
>>> &SUBSYS
>>> &COORD
>>> O -1.1328313718 10.0971039697 4.5085235925
>>> <(508)%20523-5925>
>>> O 1.8645309918 <(864)%20530-9918> 10.5352435516
>>> 3.7733787355 <(773)%20378-7355>
>>> C 2.7030432388 10.2203855181 <(220)%20385-5181>
>>> 4.6876435603
>>> C 4.1732700867 9.9603189034 1.0240943453
>>> N 2.8991506163 10.6883182415 1.2661442475
>>> H 3.9854861761 <(985)%20486-1761> 8.8739388700
>>> <(873)%20938-8700> 1.1431701506
>>> H -0.1880085309 10.2628351377 <(262)%20835-1377>
>>> 1.7874169762 <(787)%20416-9762>
>>> H 2.5508970088 10.5678906795 <(567)%20890-6795>
>>> 2.2794640551 <(279)%20464-0551>
>>> H 2.1299266928 10.3641615204 0.6076422197
>>> <(607)%20642-2197>
>>> H 3.0355380187 11.7149503356 <(714)%20950-3356>
>>> 1.0956837331
>>> O 0.2606135541 <(260)%20613-5541> 4.1119106453
>>> 2.9854064333
>>> O 3.8059402904 <(805)%20940-2904> 1.3754030821
>>> 0.4432319990
>>> O 2.4246532736 <(424)%20653-2736> 7.3594937890
>>> 1.9733323490
>>> O 2.3647100089 <(364)%20710-0089> 4.5496885449
>>> 3.7203336584
>>> O 0.8073869327 <(807)%20386-9327> 0.9362711870
>>> 1.1791992342
>>> O 0.3209465658 <(320)%20946-5658> 6.9222083110
>>> 1.2370796929
>>> C 1.5263587691 <(526)%20358-7691> 4.2364145539
>>> 2.8055072683
>>> C -0.0298900411 1.2505936711 <(250)%20593-6711>
>>> 0.2639322440
>>> C 1.1586465418 7.2354266340 2.1521597838
>>> C 2.0748435303 3.9782020732 <(978)%20202-0732>
>>> 1.3974806427
>>> C -1.4989951659 1.5076254688 <(507)%20625-4688>
>>> 3.9269434344
>>> C 0.6084458523 <(608)%20445-8523> 7.4957060596
>>> 3.5591636722
>>> N 3.3523033727 <(352)%20303-3727> 4.7004797778
>>> 1.1566879493
>>> N -0.2233531659 <(223)%20353-1659> 0.7818337399
>>> 3.6867315127
>>> N -0.6674593665 <(667)%20459-3665> 6.7708798682
>>> 3.8005551908
>>> H 2.2573306532 2.8914381358 1.2735303210
>>> H -1.3136186778 <(313)%20618-6778> 2.5940697631
>>> 3.8040335167
>>> H 0.4223631525 8.5823245920 3.6787174197
>>> <(678)%20717-4197>
>>> H 1.3356843384 4.2876690465 0.6354452396
>>> H 2.8629392281 <(862)%20939-2281> 1.2004889105
>>> 3.1646922029
>>> H 1.3473840953 <(347)%20384-0953> 7.1914260156
>>> 4.3234611998
>>> H 3.7006445086 4.5781276394 0.1431021595
>>> H 0.1250547760 0.9025559129 <(902)%20555-9129>
>>> 2.6733222144
>>> H -1.0154320008 6.8922708873 4.8142071591
>>> <(814)%20207-1591>
>>> H 4.1207144456 4.3752557215 1.8164410371
>>> <(816)%20441-0371>
>>> H 0.5452077265 1.1075507147 4.3454883057
>>> H -1.4367080245 7.0956403426 3.1416203060
>>> H 3.2195115888 <(219)%20511-5888> 5.7276855628
>>> 1.3237379417
>>> H -0.3582206354 -0.2449531115 3.8570766124
>>> H -0.5336538126 <(533)%20653-8126> 5.7439459929
>>> 3.6326709646
>>> &end COORD
>>> &CELL
>>> SYMMETRY MONOCLINIC
>>> ABC 5.102 11.971 5.458
>>> ALPHA_BETA_GAMMA 90.0 111.71 90.0
>>> PERIODIC XYZ
>>> &END CELL
>>> &KIND C
>>> BASIS_SET DZVP-GTH-PBE
>>> POTENTIAL GTH-PBE
>>> &END KIND
>>> &KIND O
>>> BASIS_SET DZVP-GTH-PBE
>>> POTENTIAL GTH-PBE
>>> &END KIND
>>> &KIND N
>>> BASIS_SET DZVP-GTH-PBE
>>> POTENTIAL GTH-PBE
>>> &END KIND
>>> &KIND H
>>> BASIS_SET DZVP-GTH-PBE
>>> POTENTIAL GTH-PBE
>>> &END KIND
>>> &END SUBSYS
>>> &END FORCE_EVAL
>>> &MOTION
>>> &GEO_OPT
>>> TYPE MINIMIZATION
>>> KEEP_SPACE_GROUP true
>>> OPTIMIZER BFGS
>>> MAX_ITER 500
>>> &END GEO_OPT
>>> &CELL_OPT
>>> KEEP_SPACE_GROUP true
>>> KEEP_SYMMETRY true
>>> &end cell_opt
>>> &PRINT
>>> &RESTART ON
>>> &EACH
>>> GEO_OPT 50
>>> &END EACH
>>> &END RESTART
>>> &END PRINT
>>> &END MOTION
>>> &VIBRATIONAL_ANALYSIS
>>> INTENSITIES true
>>> &PRINT
>>> &PROGRAM_RUN_INFO ON
>>> &END
>>> &MOLDEN_VIB
>>> FILENAME=alpha-geo-freq-700-60-6.mol
>>> &END
>>> &END
>>> &END VIBRATIONAL_ANALYSIS
>>>
>>> ************************************************************************************
>>> Any comment would be appreciated.
>>>
>>> Kindest regards,
>>> Mozhdeh
>>>
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>>>
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