[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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