[CP2K-user] [CP2K:21300] Cons Qty in Metadynamics
James Hanson
jhanson0035 at gmail.com
Wed Mar 19 14:30:25 UTC 2025
Hello CP2K community!
I am relatively new to AIMD, with only around 6 months of practice. I am
currently on a project investigating activated reactions of CO2 with
various mineral phases and am trying to produce some simple metadynamic
simulations before proceeding to more complicated reactions with multiple
CVs. The investigation I am doing today is for the reaction:
CO2(dry)+Ca(OH)2 <-> Ca(OH)(HCO3) (i.e. CO2 forming a bicarbonate on a
surface of portlandite, see attached animation I got from my NEB
calculation). I ran an NVT (see attached nvt.in) to stabilize the system
before proceeding to a metadynamics run (see met.in). During my NVT run,
the "Cons Qty" did not vary significantly (<0.001 eV) or drift at all, a
good sign! Moreover, the temperature fluctuations occured with the
deviation expected: T_mean/sqrt(nat) (see nvt_stable.png), all well and
good! Then I ran my metadynamics and I found that although the desired
reaction was indeed slowly occurring, there was an uptick in my
temperature, my potential energy, and more importantly a rise in my Cons
Qty (see metadyn.png for the first couple hundred fs or so of my metadynics
run and you can see the Cons Qty in black rise away from the equilibrium
Cons Qty I had during my NVT in red). I have two questions please:
1.) What actually is Cons Qty? Why specifically are the upticks happening?
Are these upticks meant to coincide with the height of my gaussians?
2.) Do i want Cons Qty to remain constant during my metadynamics run just
as in my NVT run? If so, how can i achieve this?
Thank you very much for any help here! If anyone is up around Scotland,
reach out and we can grab a pint!
Kindest regards,
James
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@SET DO_RESTART YES
&GLOBAL
RUN_TYPE MD
PROJECT_NAME nvt
&END GLOBAL
&FORCE_EVAL
METHOD Quickstep
&SUBSYS
&KIND Ca
BASIS_SET ORB DZVP-MOLOPT-PBE-GTH-q10
POTENTIAL GTH-PBE-q10
&END KIND
&KIND O
BASIS_SET ORB DZVP-MOLOPT-PBE-GTH-q6
POTENTIAL GTH-PBE-q6
&END KIND
&KIND H
BASIS_SET ORB DZVP-MOLOPT-PBE-GTH-q1
POTENTIAL GTH-PBE-q1
&END KIND
&KIND C
BASIS_SET ORB DZVP-MOLOPT-PBE-GTH-q4
POTENTIAL GTH-PBE-q4
&END KIND
&CELL
A 10.850066031 0.000658669 0.083340847
B -5.424474593 9.398863300 -0.048913337
C 0.296509001 -0.030263856 34.232310953
&END CELL
&COORD
SCALED
C 0.4703736849 0.5701961674 0.2058670856
O 0.3590334705 0.5228442406 0.2321309288
O 0.5925388310 0.6261189054 0.2184335940
Ca 0.0069607142 -0.0008271591 -0.0123298568
O 0.1165833872 0.2214420079 0.0215699618
O 0.2278456959 0.1082909317 0.1003396289
H 0.1161718833 0.2181045113 0.0499088091
H 0.2300329424 0.1038630517 0.0720051229
Ca 0.0038185520 -0.0008487632 0.1344767929
O 0.1174783873 0.2238846802 0.1678661298
O 0.2314378281 0.1098634306 0.9550448739
H 0.1121442331 0.2087224430 0.1958091664
H 0.2337798219 0.1091239077 0.9267796069
Ca 0.0070241171 0.3324846777 -0.0116940345
O 0.1164034977 0.5551171708 0.0214725558
O 0.2266855252 0.4433646729 0.1011513954
H 0.1154867506 0.5586901366 0.0498210537
H 0.2219816831 0.4401234627 0.0728180334
Ca 0.0031984631 0.3323095608 0.1361013741
O 0.1183951499 0.5567888117 0.1681457575
O 0.2307072673 0.4434015500 0.9550088859
H 0.1071224551 0.5701210411 0.1957107716
H 0.2312620601 0.4433094420 0.9267375037
Ca 0.0069932901 0.6656149541 -0.0125623009
O 0.1153152593 0.8873621054 0.0216129233
O 0.2273682771 0.7800413205 0.1001848589
H 0.1082136054 0.8841986846 0.0499457558
H 0.2293023218 0.7857860279 0.0718637474
Ca 0.0039004928 0.6663206552 0.1343954693
O 0.1141069189 0.8887164288 0.1675648441
O 0.2317561750 0.7776566942 0.9549911218
H 0.1068955161 0.8863754798 0.1957991022
H 0.2348429945 0.7796206661 0.9267338266
Ca 0.3403492610 -0.0008546093 -0.0113184027
O 0.4500489954 0.2219709636 0.0217405498
O 0.5615562088 0.1107135457 0.1014587760
H 0.4518718226 0.2265623006 0.0500828182
H 0.5578571250 0.1091632258 0.0731249043
Ca 0.3385613482 0.0005261108 0.1356238599
O 0.4464750768 0.2253837580 0.1674644477
O 0.5633557934 0.1097937962 0.9550215870
H 0.4451231297 0.2282889260 0.1957378543
H 0.5628229700 0.1092348611 0.9267581848
Ca 0.3406069315 0.3326558531 -0.0120205721
O 0.4496131328 0.5547314457 0.0219331785
O 0.5605162422 0.4451871029 0.1018546973
H 0.4456671450 0.5529467269 0.0502929978
H 0.5666902977 0.4523251981 0.0735548267
Ca 0.3338913725 0.3265774936 0.1321560140
O 0.4352000295 0.5508777162 0.1690749226
O 0.5647734687 0.4444784464 0.9551340590
H 0.2727049612 0.4839855903 0.2165817966
H 0.5670814853 0.4467432333 0.9268742846
Ca 0.3405654812 0.6659061317 -0.0119305477
O 0.4501777042 0.8882349728 0.0216926317
O 0.5607626524 0.7744400538 0.1016311266
H 0.4522878862 0.8872895141 0.0500311844
H 0.5670561317 0.7722881289 0.0733196820
Ca 0.3339205155 0.6693496987 0.1318353390
O 0.4464785760 0.8850325526 0.1671483515
O 0.5646624846 0.7761736208 0.9551448098
H 0.4443909693 0.8812902890 0.1954060994
H 0.5665339354 0.7747051964 0.9268819096
Ca 0.6737544392 -0.0007791151 -0.0121661960
O 0.7831106458 0.2215421006 0.0216528354
O 0.8963068878 0.1119131667 0.1012055242
H 0.7777649044 0.2190372280 0.0500026676
H 0.8986271130 0.1175215168 0.0728834870
Ca 0.6718856008 -0.0004010854 0.1349269671
O 0.7797035120 0.2212045932 0.1680310541
O 0.8977587473 0.1106352360 0.9548054116
H 0.7762930284 0.2194711947 0.1962994059
H 0.8995237885 0.1119373229 0.9265371689
Ca 0.6737507164 0.3325255893 -0.0120702898
O 0.7838836825 0.5547704144 0.0217237297
O 0.8962198753 0.4436594781 0.1013244847
H 0.7875122930 0.5531482060 0.0500297113
H 0.8978683015 0.4389922245 0.0729917712
Ca 0.6720112890 0.3336309328 0.1351732313
O 0.7850779396 0.5546209795 0.1670858716
O 0.8974765810 0.4427310292 0.9547360483
H 0.7638391754 0.5630192935 0.1942942603
H 0.8986281179 0.4412809836 0.9264689308
Ca 0.6739036294 0.6659498409 -0.0111766179
O 0.7836120485 0.8890706140 0.0217681213
O 0.8939344382 0.7765971732 0.1007334935
H 0.7869326886 0.8952634531 0.0500874612
H 0.8904313706 0.7743860063 0.0723859005
Ca 0.6759269040 0.6684966020 0.1360668368
O 0.7840459997 0.8927982227 0.1670295331
O 0.8963657605 0.7763480413 0.9549002203
H 0.7662958867 0.8681626384 0.1944992053
H 0.8946338002 0.7752944123 0.9266468256
&END COORD
&END SUBSYS
&DFT
BASIS_SET_FILE_NAME ../../../../test/BASIS_SET
POTENTIAL_FILE_NAME ../../../../test/GTH_POTENTIALS
&QS
EPS_DEFAULT 1.0E-7
&END QS
&MGRID
NGRIDS 4
CUTOFF 250
REL_CUTOFF 50
&END MGRID
&XC
&XC_FUNCTIONAL PBE
&END XC_FUNCTIONAL
&END XC
&SCF
SCF_GUESS ATOMIC
EPS_SCF 1.0E-5
MAX_SCF 300
&DIAGONALIZATION ON
ALGORITHM STANDARD
&END DIAGONALIZATION
&MIXING T
METHOD BROYDEN_MIXING
ALPHA 0.2
BETA 0.2
&END MIXING
&END SCF
&END DFT
&PRINT
&FORCES ON
&END FORCES
&END PRINT
&END FORCE_EVAL
&MOTION
&MD
ENSEMBLE NVT
STEPS 3000
TIMESTEP 0.75
TEMPERATURE 373.0
!TEMP_TOL 50
&THERMOSTAT
&NOSE
LENGTH 10
YOSHIDA 3
TIMECON 250.0
MTS 2
&END NOSE
&END
&PRINT
&ENERGY
&EACH
MD 1
&END
&END
&PROGRAM_RUN_INFO
&EACH
MD 1
&END
&END
FORCE_LAST
&END PRINT
&END MD
&END MOTION
@IF ( ${DO_RESTART} == YES )
&EXT_RESTART
RESTART_FILE_NAME nvt-1.restart
RESTART_COUNTERS T
RESTART_POS T
RESTART_VEL T
RESTART_THERMOSTAT T
&END EXT_RESTART
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@SET DO_RESTART YES
&GLOBAL
RUN_TYPE MD
PROJECT_NAME met
&END GLOBAL
&FORCE_EVAL
METHOD Quickstep
&SUBSYS
&COLVAR
&DISTANCE
ATOMS 1 50
&END DISTANCE
&END COLVAR
&COLVAR
&COORDINATION
KINDS_FROM C
KINDS_TO O !I started from Ca(OH)(CO2), this is bond lengthening between the carbon and surface
R_0 [angstrom] 1.8
NN 8
ND 14
&END COORDINATION
&END COLVAR
&KIND Ca
BASIS_SET ORB DZVP-MOLOPT-PBE-GTH-q10
POTENTIAL GTH-PBE-q10
&END KIND
&KIND O
BASIS_SET ORB DZVP-MOLOPT-PBE-GTH-q6
POTENTIAL GTH-PBE-q6
&END KIND
&KIND H
BASIS_SET ORB DZVP-MOLOPT-PBE-GTH-q1
POTENTIAL GTH-PBE-q1
&END KIND
&KIND C
BASIS_SET ORB DZVP-MOLOPT-PBE-GTH-q4
POTENTIAL GTH-PBE-q4
&END KIND
&CELL
A 10.850066031 0.000658669 0.083340847
B -5.424474593 9.398863300 -0.048913337
C 0.296509001 -0.030263856 34.232310953
&END CELL
&COORD
SCALED
C 0.4703736849 0.5701961674 0.2058670856 !I started from Ca(OH)(CO2)
O 0.3590334705 0.5228442406 0.2321309288
O 0.5925388310 0.6261189054 0.2184335940
Ca 0.0069607142 -0.0008271591 -0.0123298568
O 0.1165833872 0.2214420079 0.0215699618
O 0.2278456959 0.1082909317 0.1003396289
H 0.1161718833 0.2181045113 0.0499088091
H 0.2300329424 0.1038630517 0.0720051229
Ca 0.0038185520 -0.0008487632 0.1344767929
O 0.1174783873 0.2238846802 0.1678661298
O 0.2314378281 0.1098634306 0.9550448739
H 0.1121442331 0.2087224430 0.1958091664
H 0.2337798219 0.1091239077 0.9267796069
Ca 0.0070241171 0.3324846777 -0.0116940345
O 0.1164034977 0.5551171708 0.0214725558
O 0.2266855252 0.4433646729 0.1011513954
H 0.1154867506 0.5586901366 0.0498210537
H 0.2219816831 0.4401234627 0.0728180334
Ca 0.0031984631 0.3323095608 0.1361013741
O 0.1183951499 0.5567888117 0.1681457575
O 0.2307072673 0.4434015500 0.9550088859
H 0.1071224551 0.5701210411 0.1957107716
H 0.2312620601 0.4433094420 0.9267375037
Ca 0.0069932901 0.6656149541 -0.0125623009
O 0.1153152593 0.8873621054 0.0216129233
O 0.2273682771 0.7800413205 0.1001848589
H 0.1082136054 0.8841986846 0.0499457558
H 0.2293023218 0.7857860279 0.0718637474
Ca 0.0039004928 0.6663206552 0.1343954693
O 0.1141069189 0.8887164288 0.1675648441
O 0.2317561750 0.7776566942 0.9549911218
H 0.1068955161 0.8863754798 0.1957991022
H 0.2348429945 0.7796206661 0.9267338266
Ca 0.3403492610 -0.0008546093 -0.0113184027
O 0.4500489954 0.2219709636 0.0217405498
O 0.5615562088 0.1107135457 0.1014587760
H 0.4518718226 0.2265623006 0.0500828182
H 0.5578571250 0.1091632258 0.0731249043
Ca 0.3385613482 0.0005261108 0.1356238599
O 0.4464750768 0.2253837580 0.1674644477
O 0.5633557934 0.1097937962 0.9550215870
H 0.4451231297 0.2282889260 0.1957378543
H 0.5628229700 0.1092348611 0.9267581848
Ca 0.3406069315 0.3326558531 -0.0120205721
O 0.4496131328 0.5547314457 0.0219331785
O 0.5605162422 0.4451871029 0.1018546973
H 0.4456671450 0.5529467269 0.0502929978
H 0.5666902977 0.4523251981 0.0735548267
Ca 0.3338913725 0.3265774936 0.1321560140
O 0.4352000295 0.5508777162 0.1690749226
O 0.5647734687 0.4444784464 0.9551340590
H 0.2727049612 0.4839855903 0.2165817966
H 0.5670814853 0.4467432333 0.9268742846
Ca 0.3405654812 0.6659061317 -0.0119305477
O 0.4501777042 0.8882349728 0.0216926317
O 0.5607626524 0.7744400538 0.1016311266
H 0.4522878862 0.8872895141 0.0500311844
H 0.5670561317 0.7722881289 0.0733196820
Ca 0.3339205155 0.6693496987 0.1318353390
O 0.4464785760 0.8850325526 0.1671483515
O 0.5646624846 0.7761736208 0.9551448098
H 0.4443909693 0.8812902890 0.1954060994
H 0.5665339354 0.7747051964 0.9268819096
Ca 0.6737544392 -0.0007791151 -0.0121661960
O 0.7831106458 0.2215421006 0.0216528354
O 0.8963068878 0.1119131667 0.1012055242
H 0.7777649044 0.2190372280 0.0500026676
H 0.8986271130 0.1175215168 0.0728834870
Ca 0.6718856008 -0.0004010854 0.1349269671
O 0.7797035120 0.2212045932 0.1680310541
O 0.8977587473 0.1106352360 0.9548054116
H 0.7762930284 0.2194711947 0.1962994059
H 0.8995237885 0.1119373229 0.9265371689
Ca 0.6737507164 0.3325255893 -0.0120702898
O 0.7838836825 0.5547704144 0.0217237297
O 0.8962198753 0.4436594781 0.1013244847
H 0.7875122930 0.5531482060 0.0500297113
H 0.8978683015 0.4389922245 0.0729917712
Ca 0.6720112890 0.3336309328 0.1351732313
O 0.7850779396 0.5546209795 0.1670858716
O 0.8974765810 0.4427310292 0.9547360483
H 0.7638391754 0.5630192935 0.1942942603
H 0.8986281179 0.4412809836 0.9264689308
Ca 0.6739036294 0.6659498409 -0.0111766179
O 0.7836120485 0.8890706140 0.0217681213
O 0.8939344382 0.7765971732 0.1007334935
H 0.7869326886 0.8952634531 0.0500874612
H 0.8904313706 0.7743860063 0.0723859005
Ca 0.6759269040 0.6684966020 0.1360668368
O 0.7840459997 0.8927982227 0.1670295331
O 0.8963657605 0.7763480413 0.9549002203
H 0.7662958867 0.8681626384 0.1944992053
H 0.8946338002 0.7752944123 0.9266468256
&END COORD
&END SUBSYS
&DFT
BASIS_SET_FILE_NAME ../../../../test/BASIS_SET
POTENTIAL_FILE_NAME ../../../../test/GTH_POTENTIALS
&QS
EPS_DEFAULT 1.0E-7
&END QS
&MGRID
NGRIDS 4
CUTOFF 250
REL_CUTOFF 50
&END MGRID
&XC
&XC_FUNCTIONAL PBE
&END XC_FUNCTIONAL
&END XC
&SCF
SCF_GUESS ATOMIC
EPS_SCF 1.0E-5
MAX_SCF 300
&DIAGONALIZATION ON
ALGORITHM STANDARD
&END DIAGONALIZATION
&MIXING T
METHOD BROYDEN_MIXING
ALPHA 0.2
BETA 0.2
&END MIXING
&END SCF
&END DFT
&PRINT
&FORCES ON
&END FORCES
&END PRINT
&END FORCE_EVAL
&MOTION
&MD
ENSEMBLE NVT
STEPS 1500
TIMESTEP 0.75
TEMPERATURE 373.0
!TEMP_TOL 50
&THERMOSTAT
&NOSE
LENGTH 10
YOSHIDA 3
TIMECON 250.0
MTS 2
&END NOSE
&END
&PRINT
&ENERGY
&EACH
MD 1
&END
&END
&PROGRAM_RUN_INFO
&EACH
MD 1
&END
&END
FORCE_LAST
&END PRINT
&END MD
&FREE_ENERGY
&METADYN
DO_HILLS T
LAGRANGE !lagrange scheme requires mass
NT_HILLS 20
SLOW_GROWTH
TEMPERATURE 373
WW 0.001
HILL_TAIL_CUTOFF 2
P_EXPONENT 4
Q_EXPONENT 10
&METAVAR
MASS 50
COLVAR 1
SCALE 0.18
LAMBDA 0.8
&END METAVAR
&METAVAR
MASS 50
COLVAR 2
SCALE 0.18
LAMBDA 0.8
&END METAVAR
&PRINT
&COLVAR
COMMON_ITERATION_LEVELS 3
&EACH
MD 1
&END
&END
&END
&END METADYN
&END FREE_ENERGY
&END MOTION
@IF ( ${DO_RESTART} == YES )
&EXT_RESTART
RESTART_FILE_NAME met-1.restart
RESTART_COUNTERS T
RESTART_POS T
RESTART_VEL T
RESTART_THERMOSTAT T
&END EXT_RESTART
@ENDIF
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