[CP2K:2467] cannot restart with constraint/restraint
Liu
xiand... at gmail.com
Thu Dec 10 09:46:49 UTC 2009
2009/12/10 Teodoro Laino <teodor... at gmail.com>
> Liu wrote:
> > It is a metal-water complex. At that time, I thought it was
> > convenient to use MOLECULE keyword. now I saw the restart doesnot work
> > (even only with the velocity and position).
> I really doubt the accuracy of this statement. If you restart only
> velocity and position it will work! The problem is that you probably do
> not know how to restart only positions and velocities. The correct
> syntax would be:
>
> &EXT_RESTART
> RESTART_FILE_NAME <my_wonderful_BIG_BANG.restart>
> DEFAULT_RESTART FALSE
> RESTART_POS
> RESTART_VEL
> &END
>
> where the RESTART_DEFAULT is set to FALSE.
> >
> > I just tried with INTERMOLECULAR. The restart works!
> It works because your colvar are not expected to be on the same molecule.
> Your topology is still wrong. If you do a QS run probably (but this is
> not always the case) you do not need to specify any
> topology. To disable the construction of the connectivity:
>
>
yes, it is a QS run. it is clear on the inputfile shown above.
> &TOPOLOGY
> CONNECTIVITY OFF
> ...
> &END
> >
> > why? and why not for all?
> > Because I was lazy.
> I would never go to a doctor or a surgeon which is worldwide famous to
> be lazy.
> I could just not trust his work.
>
> Teo
>
> >
> > 2009/12/10 Teodoro Laino <teodor... at gmail.com
> > <mailto:teodor... at gmail.com>>
> >
> > 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>
> > > <mailto: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>> <mailto: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>>
> > > > <mailto: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
> > > > >
> > > > > --
> > > > >
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> >>
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> >>
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>
>
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