vmd教程 forces-tutorial(17)
发布时间:2021-06-05
发布时间:2021-06-05
vmd教程 forces-tutorial
1TCLFORCES173Nowopenthescriptrot-c.tcl.The rstdi erencesstartatline58.We rstsetupaforceslist,whichisavariabletoholdthevaluesoftheforceswewillapplytotheatoms.Wealsosetupsomecountervariables:forcecountandprintcountarebothincrementedeachtimestep.WhenforcecountequalsforcesRecalcFreq,theforcesarerecalculated,andforcecountisresettozero,asseenbelow.
setforces{}
foreachindex$atoms{
lappendforces"0.00.00.0"
}
setforcecount$forcesRecalcFreq
setprintcount0
4Nowwebeginthecalcforcescommand.First,asusual,wedeclareourglobalvariables.Wethenapplytheforcesthataresavedintheforceslist.
proccalcforces{}{
globalatomsnumatomsforcemultmassesavgmassforces
globalforcesRecalcFreq
globalforcecountprintcount
foreachatom$atomsforce$forces{
addforce$atom$force
}
5Next,wetestwhethertheforceswillberecalculatednexttimestep,andifso,tellNAMDthatwewillwantatomiccoordinatesforthetargetatomsbycallingaddatom:
if{$forcecount==[expr$forcesRecalcFreq-1]}{
print"Addingatomspriortoreconfiguringforcesat\
$printcount"
foreachatom$atoms{
addatom$atom
}
}
Aswewillseeshortly,wecallclearconfigaftertheforcesarerecalcu-lated.Thiscallerasesalladdatomrecords;withoutit,thecoordinatesoftheatomsaddedwillbeavailableeverytimestep,independentlyofwhetherwecallloadcoords,andthereforemuchofthepotentialspeedgainwillbelost.However,thismeansthataddatommustbecalledagaineachtimewewanttorecalculateforces,andbecauseoftechnicaldetailsithastobedoneatleastonestepbeforethecoordinateswillbeused.
6Nextwehavethecodethatrecalculatestheforce.Asalludedtoabove,therecalculationhappenswhenforcecountequalsforcesRecalcFreq.
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