[CP2K:2464] cannot restart with constraint/restraint
Teodoro Laino
teodor... at gmail.com
Thu Dec 10 09:00:10 UTC 2009
I see in your coord section you specify a molname for only few atoms:
why? and why not for all?
Liu wrote:
> Hi Teo,
>
> What I want to do is to restrain the 3 colvars to the respective
> target values.
> So the connectivity does not matter.
>
> Liu.
>
> 2009/12/10 Teodoro Laino <teodor... at gmail.com
> <mailto:teodor... at gmail.com>>
>
> It is not a matter of using a specific keyword. It is a matter of
> understanding what you are doing.
> If you specify INTERMOLECULAR the topology will still be built:
> you may
> not get that error but the problem is still there.
>
> I see in your coord section you specify a molname for only few atoms:
> why? and why not for all?
> do you wish to have a connectivity built or not?
> do you want to specify a restraint for intermolecular or
> intramolecular ?
> in short words: what do you want to do?
>
> Teo
>
> Liu wrote:
> >
> > 1) is ruled out. the restraint was there, so the geometry didnot
> explode.
> >
> > 2).INTERMOLECULER
> > Maybe I should have used this keyword ?
> > So no connectivity was needed any longer .
> >
> > Am I right ?
> >
> > Liu
> >
> > 2009/12/10 Liu <xiand... at gmail.com
> <mailto:xiand... at gmail.com> <mailto:xiand... at gmail.com
> <mailto:xiand... at gmail.com>>>
> >
> > Hi Teo,
> >
> > the input is as follows,
> >
> >
> > &FORCE_EVAL
> > METHOD Quickstep
> >
> > &DFT
> > POTENTIAL_FILE_NAME GTH_POTENTIALS
> > BASIS_SET_FILE_NAME GTH_BASIS_SETS
> > CHARGE 2
> > &MGRID
> > CUTOFF 320
> > &END MGRID
> > &QS
> > EPS_DEFAULT 1.0E-12
> > &END QS
> > &SCF
> > &OT T
> > MINIMIZER DIIS
> > &END OT
> > EPS_SCF 1.0E-6
> >
> > SCF_GUESS RESTART
> > MAX_SCF 110
> > &END SCF
> > &XC
> > &XC_FUNCTIONAL BLYP
> > &END XC_FUNCTIONAL
> > &END XC
> > &END DFT
> > &SUBSYS
> > &CELL
> > ABC 10.50 10.50 10.50
> > ALPHA_BETA_GAMMA 90.0000 90.0000 90.0000
> > &END CELL
> >
> > &COLVAR
> > &DISTANCE
> > ATOMS 13 1
> > &END DISTANCE
> > &END COLVAR
> > &COLVAR
> > &ANGLE
> > ATOMS 13 1 14
> > &END ANGLE
> > &END COLVAR
> > &COLVAR
> > &ANGLE
> > ATOMS 13 1 19
> > &END ANGLE
> > &END COLVAR
> > &COORD
> > O 4.945624262365 5.235220805899
> 8.003244927409 mol
> > O 4.007891695360 3.552175895176
> 5.977360545441 mol
> > O 2.285433270467 5.417764639023
> 6.897323134184 mol
> > O 5.936765184537 5.829000559392
> 5.593775858772 mol
> > O 4.183440185942 7.470635689797
> 6.674994934445 mol
> > O 3.439793446681 5.742570923209
> 4.488746955268 mol
> > H 1.793348652560 4.673685333363
> 6.448632172866 mol
> > H 1.975552174635 5.586491381857
> 7.823579691797 mol
> > H 6.341196051434 6.210453911837
> 4.735768436262 mol
> > H 6.691670293500 5.986498079468
> 6.262057248960 mol
> > H 3.355172624465 7.888242164427
> 6.980928704617 mol
> > H 4.800145134415 8.144564641311
> 6.279932035506 mol
> > H1 5.024438896426 4.333073695541
> 8.420372999423 mol
> > H 5.417966958607 5.879810696856
> 8.656369353769 mol
> > H 4.044612590192 5.703785764108
> 3.692496314811 mol
> > H 2.635152794031 6.238242225502
> 4.179846355098 mol
> > H 4.789074411431 2.978145753930
> 6.248397019420 mol
> > H 3.308516986446 3.025660313636
> 5.420256518302 mol
> > Al 4.199165250044 5.577278113875 6.261316460312
> > mol
> > O 1.929962666627 2.386347797671 4.459074121571
> > O 1.952979070957 0.358546555482 9.269519490418
> > O 0.026958456120 2.197269503272 8.735038598236
> > O -1.362279675283 6.955540825025 1.744054996031
> > O -2.899500082333 1.789177922013 2.425421734762
> > O -2.274297024247 5.797133615346 7.045592606844
> > O 1.445305003994 7.051219378572 3.715192156899
> > O 0.940001451447 4.990446887363 9.698689854397
> > O 0.031348798328 11.381839465447 1.904616048439
> > O -3.581560970691 9.411668100190 12.775652442937
> > O -1.647961298578 9.922630983793 8.321980647542
> > O 0.106325557834 -1.237262561258 0.213551451909
> > O 4.599334494386 0.610540436556 2.704211560407
> > O 6.110865497086 2.836144155293 9.037244996699
> > O 8.444963101791 12.757951977677 5.545652221781
> > O 4.717343810939 5.987976596723 1.780097066543
> > O 6.784715588065 6.889213503169 3.276373325092
> > O 0.383247580198 14.072985902428 6.230493216461
> > O 3.234318655214 3.857825154773 0.818868910110
> > O 1.963164530700 8.951099554455 7.068571426781
> > O 6.144029555568 6.796223574397 9.580179213359
> > O 8.048882212076 9.883185225311 4.810587174940
> > O 2.473675663501 10.303668237070 4.613284200787
> > O 3.999780862821 1.198425534797 0.139239985704
> > O 5.918103249911 1.825332131822 6.347934161668
> > O 5.870936669144 -0.907093857702 6.224645660032
> > O 8.497631912579 3.194191743002 -0.218198563998
> > O 10.562268276538 4.605445613458 2.706189110743
> > O 9.937102032317 8.200210165838 6.102555829864
> > O 8.599241385563 5.812668445953 9.929894326533
> > O 2.711405118216 8.000171931520 11.614265439006
> > O 6.448641165374 9.853545022641 10.091854412172
> > H 2.094505467531 1.370769732124 4.450185540604
> > H 1.766899467254 2.576096119515 3.490475988652
> > H 1.282647036726 -0.136316253288 9.811359473370
> > H 2.655785237669 0.719499451687 9.879362070408
> > H -0.608993486319 2.410722591791 9.424195138941
> > H 0.567781798217 1.367820187953 8.901435796804
> > H -0.746695201051 7.579922756681 1.272004746797
> > H -0.756268349803 6.209154398982 2.121980920129
> > H -2.895078695179 0.880540905683 2.018484814746
> > H -3.812114079147 1.945095390040 2.723542853332
> > H -1.450477955480 5.414594613020 6.547688311675
> > H -2.100265303911 5.762411444564 7.988207299506
> > H 0.856199581228 7.443072324347 4.447509731648
> > H 1.683787441702 7.732202944333 3.062648462236
> > H 0.914577100384 3.982820700161 9.483944679985
> > H -0.013545868383 5.297204143626 9.652724302908
> > H 0.842855940551 11.867508142867 1.624433490893
> > H -0.554679549011 12.094267611684 2.329428790545
> > H -3.648772260742 9.475561082667 11.749156370492
> > H -3.946707998081 8.505718208125 13.033750646306
> > H -1.349673886536 10.831974112009 7.968158045454
> > H -1.467941976087 9.098874977651 7.662349937164
> > H -0.157891145685 -0.548152766129 0.913773510052
> > H -0.486176442427 -1.036451242486 -0.545737942048
> > H 5.285066261429 -0.057476231123 2.694625810112
> > H 4.079966836623 0.551927307125 3.573612525248
> > H 6.015753238192 2.297712230229 8.175869506495
> > H 5.470262328903 2.382741162434 9.713210640781
> > H 9.282217259184 13.252061003334 5.800368726315
> > H 8.310801713089 13.069470210375 4.633682212258
> > H 4.392983089723 5.075736957232 1.274546475430
> > H 3.981000248919 6.671489138137 1.565186021664
> > H 7.666107418592 6.715687507639 2.810668805098
> > H 6.049329065526 6.466893192597 2.736263305956
> > H 0.792787273346 13.490990322042 5.543123131905
> > H 0.418620204652 13.482889458348 7.083779005514
> > H 2.540452439292 4.509285556271 0.546998335709
> > H 3.399993082999 3.414505470904 -0.002840227708
> > H 1.032218251313 8.673654190202 7.041983379026
> > H 2.094522687566 9.533513585930 7.911335251137
> > H 5.836279591854 6.578895551319 10.522628960955
> > H 7.128416505935 6.551955664875 9.651665340638
> > H 8.334130619874 10.823573762782 5.138777207840
> > H 7.835191538334 10.053541130268 3.845182999807
> > H 2.002893030136 9.680973570920 4.067457026619
> > H 2.302316195807 10.008164610561 5.548627414794
> > H 4.271980573949 1.089340786239 1.114383694195
> > H 4.742087428870 0.658613977652 -0.337748849214
> > H 5.834805046820 0.889378508637 6.043605489317
> > H 6.885651604423 2.000027177721 6.057665925746
> > H 6.514304273259 -0.920000002808 6.971136480943
> > H 6.480216340233 -0.978037422098 5.424181543392
> > H 7.718541069821 3.011662500946 -0.863906539993
> > H 8.130716210257 2.931264814758 0.649970337419
> > H 11.396873489626 5.053367889582 2.899398079628
> > H 10.639341197546 4.446886981342 1.681298091029
> > H 9.275748751503 8.741134402620 5.594644857244
> > H 9.508184542015 7.278563165823 6.211855784019
> > H 8.456691240675 4.796394786938 10.089977970213
> > H 8.591160601702 6.196940377323 10.904893066768
> > H 1.850384315640 7.951775925152 11.140192575907
> > H 2.859191674027 8.984887322643 11.845765015442
> > H 6.092174319778 8.925042319655 9.772217739704
> > H 7.222986151208 9.962961083214 9.512548867753
> > &END COORD
> > &KIND H
> > BASIS_SET TZV2P-GTH
> > POTENTIAL GTH-BLYP-q1
> > &END KIND
> > &KIND H1
> > BASIS_SET NONE
> > POTENTIAL GTH-BLYP-q1
> > GHOST
> > &END KIND
> > &KIND O
> > BASIS_SET TZV2P-GTH
> > POTENTIAL GTH-BLYP-q6
> > &END KIND
> > &KIND Al
> > BASIS_SET DZVP-GTH
> > POTENTIAL GTH-BLYP-q3
> > &END KIND
> >
> > &END SUBSYS
> > &END FORCE_EVAL
> > &GLOBAL
> >
> > PROJECT A
> > RUN_TYPE MD
> > PRINT_LEVEL MEDIUM
> > &PRINT
> > &EACH
> >
> > &END EACH
> > &END PRINT
> > &END GLOBAL
> > &MOTION
> >
> > &CONSTRAINT
> > &COLLECTIVE
> > TARGET 1.89
> > MOLECULE 1
> > COLVAR 1
> > &RESTRAINT
> > k 0.1
> > &END RESTRAINT
> > &END COLLECTIVE
> > &COLLECTIVE
> > TARGET 1.869
> > MOLECULE 1
> > COLVAR 2
> > &RESTRAINT
> > k 0.1
> > &END RESTRAINT
> > &END COLLECTIVE
> > &COLLECTIVE
> > TARGET 2.1457
> > MOLECULE 1
> > COLVAR 3
> > &RESTRAINT
> > k 0.1
> > &END RESTRAINT
> > &END COLLECTIVE
> > &END CONSTRAINT
> > &MD
> > ENSEMBLE NVT
> > STEPS 50000
> > TIMESTEP 0.5
> > TEMPERATURE 330.0
> >
> > &THERMOSTAT
> > &NOSE
> > LENGTH 3
> > YOSHIDA 3
> > TIMECON 1000.0
> > MTS 2
> > &END NOSE
> > &END THERMOSTAT
> > &END MD
> >
> > &PRINT
> > &TRAJECTORY
> > &EACH
> > MD 20
> > &END EACH
> > &END TRAJECTORY
> > &END PRINT
> >
> > &END MOTION
> >
> >
> > could you please give some further comment on this ?
> >
> > Thanks for your help
> >
> > Liu
> >
> > 2009/12/10 Teodoro Laino <teodor... at gmail.com
> <mailto:teodor... at gmail.com>
> > <mailto:teodor... at gmail.com
> <mailto:teodor... at gmail.com>>>
> >
> > Basically this issue has many different sources. The two
> most
> > important:
> >
> > -) The first problem is that you should seriously think
> if you
> > want
> > help: in this case next time I would recommend to send the
> > entire input
> > file and not just pieces of it.
> >
> > -) The second problem is that CP2K has not a manual: it is
> > difficult to
> > learn but we do provide (for extremely motivated people)
> quite
> > a big
> > number of working input files, which cover most of its
> > functionalities.
> > It would be ideal that before mixing keywords and
> subsections
> > you would
> > train yourself trying first to understand (on your own) what
> > is the
> > logic of the code.
> >
> > Having said that, based on the minimal amount of information
> > you sent
> > us, I can try to guess:
> >
> > 1) probably you ask cp2k to build the topology. At the
> > beginning the
> > geometry is reasonable and cp2k is able to build a correct
> > connectivity.
> > When you restart (connectivity is not restartable!) cp2k
> > builds a new
> > connectivity and very probably your input
> > file is so well tuned that the system just explodes -> new
> > connectivity
> > is a mess -> the intramolecular constraint cannot be
> applied (your
> > restratins is intramolecular!!)
> >
> > 2) with the restraint setup below (the only piece you have
> > sent) you are
> > specifying the same restraint for all molecular types 1. if
> > you want to
> > apply just 1 restraint (between two atoms not belonging
> to the
> > same
> > molecule) there is a keyword to be specified:
> >
> http://cp2k.berlios.de/manual/CP2K_INPUT/MOTION/CONSTRAINT/COLLECTIVE.html#desc_INTERMOLECULAR
> >
> > 3) if you really want to have the same restraint appled
> to all
> > molecular
> > types 1 then I would recommend you to have a topology file.
> > This will
> > guarantee that even if you are trying to simulate the "big
> > bang" the
> > specification of molecular connectivity will not depend
> on how
> > far are
> > the atoms.
> >
> > 4) if you don't need the connectivity (because your goal
> is to
> > model
> > some explosion [for example..]) then just disable the
> > generation of the
> > connectivity.
> >
> > Since the possible sources are many (because mainly we
> cannot
> > understand
> > what you really want to do!) I would suggest you : take your
> > time, think
> > what you want to do with cp2k and your present run.
> >
> > Teo
> >
> >
> > Liu wrote:
> > > Hi all,
> > >
> > > I used the following COLVAR and CONSTRAINT to do a MD run
> > and it goes
> > > well.
> > >
> > > &COLVAR
> > > &DISTANCE
> > > ATOMS 13 1
> > > &END DISTANCE
> > > &END COLVAR
> > >
> > > &CONSTRAINT
> > > &COLLECTIVE
> > > TARGET 1.89
> > > MOLECULE 1
> > > COLVAR 1
> > > &RESTRAINT
> > > k 0.1
> > > &END RESTRAINT
> > > &END COLLECTIVE
> > >
> > > &END CONSTRAINT
> > >
> > > When I added this:
> > > &EXT_RESTART
> > > RESTART_FILE_NAME A-1.restart
> > > RESTART_DEFAULT TRUE
> > > &END EXT_RESTART
> > >
> > > the error happened:
> > >
> > > | Error in constraints setup!
> > > | A constraint has been defined for a molecule type
> > > | but the atoms specified in the constraint and
> the a |
> > > Error in constraints setup!
> > > | A constraint has been defined for a molecule type
> > > | but the atoms specified in the constraint and
> the atoms
> > > defined for
> > > | the molecule DO NOT match!
> > >
> > > Any suggestion is appreciated !
> > >
> > > cheers,
> > > Liu
> > >
> > > --
> > >
> > > You received this message because you are subscribed
> to the
> > Google Groups "cp2k" group.
> > > To post to this group, send email to
> cp... at googlegroups.com <mailto:cp... at googlegroups.com>
> > <mailto:cp... at googlegroups.com
> <mailto:cp... at googlegroups.com>>.
> > > To unsubscribe from this group, send email to
> > cp2k+uns... at googlegroups.com
> <mailto:cp2k%2Bun... at googlegroups.com>
> > <mailto:cp2k%2Bun... at googlegroups.com
> <mailto:cp2k%252Bu... at googlegroups.com>>.
> > > For more options, visit this group at
> > http://groups.google.com/group/cp2k?hl=en.
> > >
> > >
> > >
> >
> > --
> >
> > You received this message because you are subscribed to the
> > Google Groups "cp2k" group.
> > To post to this group, send email to
> cp... at googlegroups.com <mailto:cp... at googlegroups.com>
> > <mailto:cp... at googlegroups.com
> <mailto:cp... at googlegroups.com>>.
> > To unsubscribe from this group, send email to
> > cp2k+uns... at googlegroups.com
> <mailto:cp2k%2Bun... at googlegroups.com>
> > <mailto:cp2k%2Bun... at googlegroups.com
> <mailto:cp2k%252Bu... at googlegroups.com>>.
> > For more options, visit this group at
> > http://groups.google.com/group/cp2k?hl=en.
> >
> >
> >
> >
> > --
> >
> > You received this message because you are subscribed to the Google
> > Groups "cp2k" group.
> > To post to this group, send email to cp... at googlegroups.com
> <mailto:cp... at googlegroups.com>.
> > To unsubscribe from this group, send email to
> > cp2k+uns... at googlegroups.com
> <mailto:cp2k%2Bun... at googlegroups.com>.
> > For more options, visit this group at
> > http://groups.google.com/group/cp2k?hl=en.
>
> --
>
> You received this message because you are subscribed to the Google
> Groups "cp2k" group.
> To post to this group, send email to cp... at googlegroups.com
> <mailto:cp... at googlegroups.com>.
> To unsubscribe from this group, send email to
> cp2k+uns... at googlegroups.com
> <mailto:cp2k%2Bun... at googlegroups.com>.
> For more options, visit this group at
> http://groups.google.com/group/cp2k?hl=en.
>
>
>
> --
>
> You received this message because you are subscribed to the Google
> Groups "cp2k" group.
> To post to this group, send email to cp... at googlegroups.com.
> To unsubscribe from this group, send email to
> cp2k+uns... at googlegroups.com.
> For more options, visit this group at
> http://groups.google.com/group/cp2k?hl=en.
More information about the CP2K-user
mailing list