psf problems
Toon
Toon.Ver... at gmail.com
Fri Jun 1 11:50:53 UTC 2007
Hi, I have a related question. Is it normal that
COORDINATE XYZ
COORD_FILE_NAME geometry.xyz
can not be used with MC simumations, or is this a problem with my
compilation of cp2k?
cheers,
Toon
On 30 mei, 08:12, Teodoro Laino <teodor... at gmail.com> wrote:
> PSF is a CHARMM standard format.. you won't find any place around
> where they specify the format..
> all the available programs reading PSF have +/- hacked the original
> format..
> so we do..
>
> teo
>
> On 30 May 2007, at 08:00, Toon wrote:
>
>
>
> > Hi Teo,
>
> > Thanks for your help. I'll update my copy of cp2k. Is there a standard
> > specification for the PSF format availlable on the internet? In the
> > (very) long run, I'd like to update my scripts to generate standard
> > psf files.
>
> > cheers,
>
> > Toon
>
> > On 29 mei, 19:40, Teodoro Laino <teodor... at gmail.com> wrote:
> >> Toon,
>
> >> from your input file I see you're using not an up2date version of
> >> cp2k.. at least 1-2 months old..
> >> I cannot offer any help for the code you are using..
>
> >> BUT if you update to the new one and use this section:
>
> >> &TOPOLOGY
> >> CONNECTIVITY MOL_SET
> >> &MOL_SET
> >> &MOLECULE
> >> NMOL 8
> >> CONN_FILE_NAME single.psf
> >> CONNECTIVITY UPSF
> >> &END
> >> &END
> >> &END TOPOLOGY
>
> >> your example works..
>
> >> Bytheway.. yours is not a standard PSF.. me and Axel were working
> >> for a couple of weeks and at the moment
> >> cp2k supports the EXT standard of the PSF.. everytime you have a psf
> >> that is not standard you need to specify
> >> that its connectivity is UPSF (mostly you don't care about the
> >> format..)
>
> >> teo
>
> >> On 29 May 2007, at 15:11, Toon wrote:
>
> >>> Hi,
>
> >>> I've been trying to run an mc simulation with the input given below.
> >>> I'm just trying to understand how this should work in cp2k. The
> >>> input
> >>> is just a dummy example. When I try to run this example (with
> >>> cp2k.sdbg), I got this error:
>
> >>> ...
> >>> PSF_INFO| Parsing the NATOM section
> >>> PSF_INFO| NATOM = 5
> >>> PSF_INFO| Parsing the NBOND section
> >>> PSF_INFO| NBOND = 4
> >>> PSF_INFO| Parsing the NTHETA section
> >>> PSF_INFO| NTHETA = 6
> >>> PSF_INFO| Parsing the NPHI section
> >>> PSF_INFO| NPHI = 0
> >>> At line 886 of file /home/toon/tmp/build/cp2k/makefiles/../src/
> >>> topology_util.F
> >>> Traceback: (Innermost first)
> >>> Called from line 498 of file /home/toon/tmp/build/cp2k/
> >>> makefiles/../
> >>> src/topology_psf.F
> >>> Called from line 359 of file /home/toon/tmp/build/cp2k/
> >>> makefiles/../
> >>> src/topology.F
> >>> Called from line 206 of file /home/toon/tmp/build/cp2k/
> >>> makefiles/../
> >>> src/topology.F
> >>> Called from line 279 of file /home/toon/tmp/build/cp2k/
> >>> makefiles/../
> >>> src/qs_environment.F
> >>> Called from line 111 of file /home/toon/tmp/build/cp2k/
> >>> makefiles/../
> >>> src/qs_main.F
> >>> Called from line 729 of file /home/toon/tmp/build/cp2k/
> >>> makefiles/../
> >>> src/f77_interface.F
> >>> Called from line 268 of file /home/toon/tmp/build/cp2k/
> >>> makefiles/../
> >>> src/cp2k_runs.F
> >>> Called from line 847 of file /home/toon/tmp/build/cp2k/
> >>> makefiles/../
> >>> src/cp2k_runs.F
> >>> Called from line 248 of file /home/toon/tmp/build/cp2k/
> >>> makefiles/../
> >>> src/cp2k.F
> >>> Fortran runtime error: Array element out of bounds: 31 in (1:5),
> >>> dim=1
>
> >>> The psf file is also given below. It describes the topology of
> >>> exactly
> >>> one of the eight methane molecules. I believe the psf file is
> >>> correct,
> >>> is it? I did take a look at the part of the code where the error
> >>> occurs but I don't really understand what it is expected to do. (It
> >>> reads the psf file, something goes wrong when processing the one-
> >>> four
> >>> pairs, but I don't get the details.) Is there something wrong in the
> >>> input/psf file or is this a bug? The examples from the regtests work
> >>> on my machine.
>
> >>> best regards,
>
> >>> Toon
>
> >>> the input file:
>
> >>> &FORCE_EVAL
>
> >>> METHOD Quickstep
> >>> &DFT
> >>> &QS
> >>> METHOD PM3
> >>> EPS_DEFAULT 1.0E-12
> >>> EPS_GVG 1.0E-6
> >>> EPS_PGF_ORB 1.0E-6
> >>> &END QS
> >>> &SCF
> >>> EPS_SCF 1.0E-6
> >>> MAX_SCF 150
> >>> SCF_GUESS atomic
> >>> &END SCF
> >>> &END DFT
>
> >>> &SUBSYS
> >>> &CELL
> >>> ABC 7.800000 7.800000 7.800000
> >>> UNIT ANGSTROM
> >>> &END CELL
> >>> &COORD
> >>> C 7.1545135964 0.2916147406 0.6622232680
> >>> H 6.6668950468 1.1504609369 1.1033507689
> >>> H 7.6334667531 0.6233226102 -0.2564860726
> >>> H 6.4208845485 -0.4795931637 0.4356274201
> >>> H 7.9005900072 -0.1048244889 1.3410306662
> >>> C 6.8528101393 3.6807499565 1.5744193983
> >>> H 6.4514929741 2.8349587584 2.1188989803
> >>> H 7.7679317225 3.4073223315 1.0559592149
> >>> H 7.0709998781 4.4961704973 2.2881955953
> >>> H 6.1341098685 4.0308814768 0.8225903997
> >>> C 1.9813613499 6.7192653419 5.8763727299
> >>> H 2.0321973418 7.4196170794 6.7046158757
> >>> H 1.2903991153 7.1400631283 5.1330330349
> >>> H 1.5834916118 5.7941607545 6.2462624125
> >>> H 2.9782222352 6.5700588933 5.4382607646
> >>> C 6.8935808834 10.9042343214 4.8896018240
> >>> H 6.9090027651 10.0556726408 5.5732300957
> >>> H 7.1082178538 11.7975226536 5.4836337927
> >>> H 5.9106655806 10.9864139714 4.4468607567
> >>> H 7.6585223681 10.7854616816 4.0984669623
> >>> C 3.4097928887 4.5767446702 2.2242443860
> >>> H 3.0529585247 4.4184677018 1.2009363529
> >>> H 3.2785552112 3.6406911435 2.7889006394
> >>> H 2.8302525350 5.3840010296 2.6917414739
> >>> H 4.4528957985 4.8811323379 2.2007501082
> >>> C 2.9805519373 8.2006034213 9.5372130039
> >>> H 3.3335722902 9.0450868984 10.1155313292
> >>> H 2.1188103649 7.7275659069 10.0272973693
> >>> H 3.7804325728 7.4372375456 9.4173176654
> >>> H 2.6890775746 8.5348163384 8.5285057129
> >>> C 6.0352120743 6.4801397125 4.0960140077
> >>> H 6.5874102060 7.3836880272 3.9041291362
> >>> H 5.4489916745 6.2452884244 3.2172777054
> >>> H 5.3670640659 6.6104228115 4.9504368037
> >>> H 6.7521214494 5.6814792763 4.3123759997
> >>> C 3.2928814788 2.5582719306 5.8498575291
> >>> H 3.0860227820 2.3159397213 6.8922542536
> >>> H 3.5005462509 3.6199393877 5.7655448415
> >>> H 2.4455631533 2.3255776287 5.2113735329
> >>> H 4.1684058503 1.9781743596 5.5368454612
> >>> &END COORD
> >>> &TOPOLOGY
> >>> CONNECTIVITY MOL_SET
> >>> &MOL_SET
> >>> NMOL 8
> >>> CONN_FILE_NAME single.psf
> >>> &END
> >>> &END TOPOLOGY
> >>> &PRINT
> >>> &TOPOLOGY_INFO
> >>> EACH 1
> >>> PSF_INFO T
> >>> &END TOPOLOGY_INFO
> >>> &END PRINT
> >>> &END SUBSYS
> >>> &END FORCE_EVAL
>
> >>> &GLOBAL
> >>> FFT_LIB FFTW3
> >>> PROJECT mc
> >>> RUN_TYPE MC
> >>> &END GLOBAL
>
> >>> &MOTION
> >>> &MC
> >>> IUPTRANS 6400000
> >>> IUPVOLUME 3200000
> >>> LBIAS no
> >>> LSTOP yes
> >>> NMOVES 8
> >>> NSTEP 2
> >>> PMSWAP 0.0
> >>> PMTRAION 0.00
> >>> PMTRANS 0.00
> >>> PMVOLUME 1.00
> >>> PMVOL_BOX 1.00
> >>> PRESSURE 1
> >>> ENSEMBLE traditional
> >>> RESTART no
> >>> RESTART_FILE_NAME mc_restart_1
> >>> RMDIHEDRAL 3.0
> >>> RMANGLE 3.0
> >>> RMBOND 0.074
> >>> RMROT 26.0
> >>> RMTRANS 0.38
> >>> RMVOLUME 0.5
> >>> TEMP 101.055000
> >>> AVBMC_RMIN 1.0
> >>> AVBMC_RMAX 5.0
> >>> AVBMC_ATOM 1
> >>> PBIAS 0.5
> >>> PMAVBMC_MOL 1.0
> >>> PMSWAP_MOL 1.0
> >>> PMROT_MOL 1.0
> >>> PMTRANS_MOL 1.0
> >>> PMTRAION_MOL 1.0
> >>> &END MC
> >>> &PRINT
> >>> &TRAJECTORY
> >>> EACH 5
> >>> &END TRAJECTORY
> >>> &END PRINT
> >>> &END MOTION
>
> >>> The file single.psf looks like this:
>
> >>> PSF
>
> >>> 1 !NTITLE
> >>> None
>
> >>> 5 !NATOM
> >>> 1 NAME 1 NAME C C 0.0 12.010700 0
> >>> 2 NAME 1 NAME H H 0.0 1.007940 0
> >>> 3 NAME 1 NAME H H 0.0 1.007940 0
> >>> 4 NAME 1 NAME H H 0.0 1.007940 0
> >>> 5 NAME 1 NAME H H 0.0 1.007940 0
>
> >>> 4 !NBOND
> >>> 2 1 3 1 4 1 5 1
>
> >>> 6 !NTHETA
> >>> 4 1 2 5 1 2 3 1 2
> >>> 5 1 4 4 1 3 5 1 3
>
> >>> 0 !NPHI
>
> >>> 0 !NIMPHI
>
> >>> 0 !NDON
>
> >>> 0 !NACC
>
> >>> 0 !NNB
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