[CP2K:2466] cannot restart with constraint/restraint
Teodoro Laino
teodor... at gmail.com
Thu Dec 10 09:25:25 UTC 2009
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:
&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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> <mailto:cp2k%252Bu... at googlegroups.com>>
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> For more options, visit this group at
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