ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Added running example of PLUMED + LAMMPS

Browse Source 
Not sure if this has been done correctly.  I add both the input and the output
This commit is contained in:
Gareth Tribello
2018-07-02 10:22:23 +01:00
parent 9b44529591
commit 2c5f2a6683
5 changed files with 178 additions and 12 deletions
Download Patch File Download Diff File Expand all files Collapse all files

102
examples/USER/plumed/colvar Normal file
View File

@ -0,0 +1,102 @@
#! FIELDS time d1 d2 h_pot.bias h_pot.force2
0.000000 0.993491 0.758366 0.292146 5.842921
0.002000 0.995476 0.759311 0.289757 5.795146
0.004000 0.997617 0.760436 0.286982 5.739638
0.006000 0.999849 0.761714 0.283902 5.678045
0.008000 1.002126 0.763111 0.280604 5.612077
0.010000 1.004429 0.764614 0.277132 5.542631
0.012000 1.006758 0.766228 0.273476 5.469523
0.014000 1.009119 0.767975 0.269594 5.391885
0.016000 1.011514 0.769873 0.265455 5.309099
0.018000 1.013929 0.771911 0.261093 5.221860
0.020000 1.016331 0.774032 0.256641 5.132826
0.022000 1.018671 0.776135 0.252321 5.046430
0.024000 1.020900 0.778094 0.248395 4.967894
0.026000 1.022979 0.779791 0.245099 4.901982
0.028000 1.024903 0.781143 0.242592 4.851832
0.030000 1.026700 0.782129 0.240904 4.818078
0.032000 1.028430 0.782795 0.239931 4.798623
0.034000 1.030167 0.783248 0.239458 4.789166
0.036000 1.031975 0.783621 0.239212 4.784241
0.038000 1.033897 0.784047 0.238923 4.778459
0.040000 1.035930 0.784627 0.238382 4.767647
0.042000 1.038033 0.785407 0.237484 4.749678
0.044000 1.040121 0.786369 0.236240 4.724809
0.046000 1.042091 0.787439 0.234768 4.695368
0.048000 1.043837 0.788511 0.233246 4.664919
0.050000 1.045280 0.789471 0.231863 4.637266
0.052000 1.046388 0.790226 0.230785 4.615694
0.054000 1.047178 0.790712 0.230136 4.602723
0.056000 1.047712 0.790891 0.230015 4.600302
0.058000 1.048083 0.790742 0.230505 4.610102
0.060000 1.048397 0.790252 0.231683 4.633662
0.062000 1.048754 0.789414 0.233618 4.672352
0.064000 1.049236 0.788230 0.236354 4.727083
0.066000 1.049892 0.786723 0.239883 4.797654
0.068000 1.050741 0.784954 0.244096 4.881918
0.070000 1.051768 0.783036 0.248766 4.975312
0.072000 1.052946 0.781120 0.253559 5.071179
0.074000 1.054246 0.779374 0.258094 5.161873
0.076000 1.055648 0.777949 0.262017 5.240331
0.078000 1.057143 0.776950 0.265083 5.301665
0.080000 1.058728 0.776406 0.267217 5.344336
0.082000 1.060397 0.776265 0.268526 5.370525
0.084000 1.062135 0.776403 0.269282 5.385630
0.086000 1.063918 0.776650 0.269855 5.397095
0.088000 1.065713 0.776818 0.270642 5.412845
0.090000 1.067486 0.776746 0.271982 5.439646
0.092000 1.069203 0.776331 0.274084 5.481685
0.094000 1.070839 0.775547 0.276987 5.539735
0.096000 1.072370 0.774448 0.280554 5.611090
0.098000 1.073779 0.773153 0.284514 5.690279
0.100000 1.075049 0.771810 0.288515 5.770295
0.102000 1.076167 0.770572 0.292193 5.843867
0.104000 1.077116 0.769571 0.295223 5.904455
0.106000 1.077882 0.768908 0.297345 5.946904
0.108000 1.078459 0.768648 0.298397 5.967949
0.110000 1.078853 0.768806 0.298342 5.966843
0.112000 1.079090 0.769340 0.297296 5.945926
0.114000 1.079219 0.770158 0.295516 5.910315
0.116000 1.079303 0.771141 0.293328 5.866561
0.118000 1.079415 0.772170 0.291067 5.821338
0.120000 1.079622 0.773135 0.289037 5.780735
0.122000 1.079971 0.773942 0.287489 5.749783
0.124000 1.080476 0.774515 0.286599 5.731971
0.126000 1.081103 0.774812 0.286437 5.728730
0.128000 1.081783 0.774828 0.286955 5.739101
0.130000 1.082421 0.774602 0.287987 5.759744
0.132000 1.082925 0.774217 0.289271 5.785430
0.134000 1.083230 0.773787 0.290498 5.809961
0.136000 1.083320 0.773437 0.291366 5.827324
0.138000 1.083229 0.773283 0.291638 5.832753
0.140000 1.083032 0.773417 0.291171 5.823427
0.142000 1.082825 0.773886 0.289936 5.798729
0.144000 1.082697 0.774694 0.288007 5.760150
0.146000 1.082716 0.775795 0.285550 5.710997
0.148000 1.082911 0.777098 0.282797 5.655945
0.150000 1.083267 0.778482 0.280018 5.600355
0.152000 1.083739 0.779816 0.277467 5.549332
0.154000 1.084258 0.780984 0.275337 5.506735
0.156000 1.084764 0.781917 0.273726 5.474524
0.158000 1.085215 0.782595 0.272633 5.452651
0.160000 1.085600 0.783050 0.271973 5.439463
0.162000 1.085939 0.783349 0.271614 5.432288
0.164000 1.086269 0.783582 0.271395 5.427907
0.166000 1.086632 0.783845 0.271141 5.422814
0.168000 1.087062 0.784236 0.270670 5.413403
0.170000 1.087575 0.784841 0.269815 5.396302
0.172000 1.088169 0.785721 0.268447 5.368936
0.174000 1.088827 0.786902 0.266506 5.330122
0.176000 1.089527 0.788366 0.264020 5.280397
0.178000 1.090249 0.790062 0.261095 5.221908
0.180000 1.090983 0.791909 0.257899 5.157988
0.182000 1.091725 0.793812 0.254634 5.092674
0.184000 1.092478 0.795671 0.251513 5.030265
0.186000 1.093252 0.797384 0.248746 4.974922
0.188000 1.094056 0.798864 0.246512 4.930235
0.190000 1.094906 0.800048 0.244938 4.898769
0.192000 1.095809 0.800909 0.244083 4.881658
0.194000 1.096763 0.801455 0.243917 4.878336
0.196000 1.097747 0.801731 0.244326 4.886516
0.198000 1.098716 0.801809 0.245123 4.902456
0.200000 1.099614 0.801777 0.246077 4.921541

64
examples/USER/plumed/p.log Normal file
View File

@ -0,0 +1,64 @@
PLUMED: PLUMED is starting
PLUMED: Version: 2.5.0-dev (git: a10584333) compiled on Jul 2 2018 at 09:29:02
PLUMED: Please cite this paper when using PLUMED [1]
PLUMED: For further information see the PLUMED web page at http://www.plumed.org
PLUMED: Root: /data/gt/mycodes/plumed2/
PLUMED: For installed feature, see /data/gt/mycodes/plumed2//src/config/config.txt
PLUMED: Molecular dynamics engine: LAMMPS
PLUMED: Precision of reals: 8
PLUMED: Running over 1 node
PLUMED: Number of threads: 1
PLUMED: Cache line size: 512
PLUMED: Number of atoms: 2004
PLUMED: File suffix:
PLUMED: FILE: plumed.dat
PLUMED: Action COM
PLUMED: with label c1
PLUMED: serial associated to this virtual atom is 2005
PLUMED: of atoms
PLUMED: 2 4 5 6
PLUMED: broken molecules will be rebuilt assuming atoms are in the proper order
PLUMED: Action COM
PLUMED: with label c2
PLUMED: serial associated to this virtual atom is 2006
PLUMED: of atoms
PLUMED: 80 82 83 84
PLUMED: broken molecules will be rebuilt assuming atoms are in the proper order
PLUMED: Action DISTANCE
PLUMED: with label d1
PLUMED: between atoms 2005 37
PLUMED: using periodic boundary conditions
PLUMED: Action DISTANCE
PLUMED: with label d2
PLUMED: between atoms 2006 37
PLUMED: using periodic boundary conditions
PLUMED: Action RESTRAINT
PLUMED: with label h_pot
PLUMED: with arguments d1 d2
PLUMED: added component to this action: h_pot.bias
PLUMED: at 1.000000 1.000000
PLUMED: with harmonic force constant 10.000000 10.000000
PLUMED: and linear force constant 0.000000 0.000000
PLUMED: added component to this action: h_pot.force2
PLUMED: Action PRINT
PLUMED: with label @5
PLUMED: with stride 1
PLUMED: with arguments d1 d2 h_pot.bias h_pot.force2
PLUMED: on file colvar
PLUMED: with format %f
PLUMED: END FILE: plumed.dat
PLUMED: Timestep: 0.002000
PLUMED: KbT has not been set by the MD engine
PLUMED: It should be set by hand where needed
PLUMED: Relevant bibliography:
PLUMED: [1] Tribello, Bonomi, Branduardi, Camilloni, and Bussi, Comput. Phys. Commun. 185, 604 (2014)
PLUMED: Please read and cite where appropriate!
PLUMED: Finished setup
PLUMED: Cycles Total Average Minumum Maximum
PLUMED: 1 0.015035 0.015035 0.015035 0.015035
PLUMED: 1 Prepare dependencies 101 0.000123 0.000001 0.000001 0.000004
PLUMED: 2 Sharing data 101 0.006837 0.000068 0.000047 0.000891
PLUMED: 3 Waiting for data 101 0.000967 0.000010 0.000007 0.000041
PLUMED: 4 Calculating (forward loop) 101 0.001616 0.000016 0.000011 0.000043
PLUMED: 5 Applying (backward loop) 101 0.002159 0.000021 0.000018 0.000057
PLUMED: 6 Update 101 0.001059 0.000010 0.000006 0.000086

4
examples/USER/plumed/plumed.dat
View File

@ -2,5 +2,5 @@ c1: COM ATOMS=2,4,5,6
c2: COM ATOMS=80,82,83,84
d1: DISTANCE ATOMS=c1,37
d2: DISTANCE ATOMS=c2,37
h_pot: RESTRAINT ARG=d1,d2 CENTER=1.0,1.0 KAPPA=10,10
PRINT ARG=d1,d2,h_pot.*
h_pot: RESTRAINT ARG=d1,d2 AT=1.0,1.0 KAPPA=10,10
PRINT ARG=d1,d2,h_pot.* FILE=colvar