lijiext
/
lammps
mirror of https://github.com/lammps/lammps.git
1
0
Fork 1
Code Issues Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2571 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2009-02-12 16:09:50 +00:00
parent 2894746c8f
commit 7f019a4b37
7 changed files with 25 additions and 19 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

7
lib/reax/README
View File

@ -28,6 +28,7 @@ library source files and the LAMMPS pair_reax.cpp source file (from
module REAX). It contains dimensions of statically-allocated arrays
created by the ReaxFF library. The size of these arrays must be set
small enough to avoid exceeding the available machine memory, and
large enough to fit the actual data generated by ReaxFF. If you
change the values in reax_defs.h, you must first rebuild the library
and then rebuild LAMMPS.
large enough to fit the actual data generated by ReaxFF. If you change
the values in reax_defs.h, you must first rebuild the library and then
rebuild LAMMPS.

1
lib/reax/cbka.blk
View File

@ -54,6 +54,7 @@
$ elmol(nmolmax),
$ elaf(nsort),vpq(nsort),
$ rvdw(nsort),alf(nsort),eps(nsort),chat(nsort),
$ rcore(nsort,nsort),ecore(nsort,nsort),acore(nsort,nsort),
$ vlp2(nsort),
$ valp2(nsort),vincr(nsort),
$ vval3(nsort),

3
lib/reax/cbkc.blk
View File

@ -1,4 +1,5 @@
common
$/cbkc/ c(nat,3),cglobal(nattot,3),itag(nat)
$/cbkc/ c(nat,3),cglobal(nattot,3),itag(nat),
$chgglobal(nattot)

15
lib/reax/reax_connect.F
View File

@ -393,7 +393,6 @@ c$$$ call mdsav(1,qfile(nprob))
* lhb controls whether or not to unprune ghost bonds that *
* may possibly form ghost hydrogen bonds. *
* Setting it to 1 causes unpruning, and so is the safe option. *
* With the new midpoint method, lhb=0 may miss some h-bonds *
* If lprune = 0, then pruning is not used, results are exact *
* and lhb has no effect. *
* *
@ -604,17 +603,19 @@ c but it does store bond entries in nubon2()
ihhb2=nphb(ia(j2,1))
end if
* Only need to compute bonds where j3 is local
* Only need to compute bonds where j1 is local
if (j1 .le. na_local) then
if (ihhb1.eq.1.and.ihhb2.eq.2) then
call dista2(j1,j2,dishb,dxm,dym,dzm)
if (dishb.lt.hbcut) then
do i23=1,ia(j1,2) !Search for acceptor atoms bound to donor atom
j3=ia(j1,2+i23)
if (nphb(ia(j3,1)).eq.2.and.j3.ne.j2) then
nboncol(nubon2(j1,i23))=-1
ntmphb = ntmphb+1
if (nboncol(nubon2(j1,i23)).eq.0) then
j3=ia(j1,2+i23)
if (nphb(ia(j3,1)).eq.2.and.j3.ne.j2) then
nboncol(nubon2(j1,i23))=-1
ntmphb = ntmphb+1
endif
endif
end do
end if
@ -1475,7 +1476,7 @@ c
ihhb2=nphb(ia(j2,1))
end if
* Only need to compute bonds where j3 is local
* Only need to compute bonds where j1 is local
if (j1 .le. na_local) then
if (ihhb1.eq.1.and.ihhb2.eq.2) then

13
lib/reax/reax_inout.F
View File

@ -33,6 +33,7 @@
#include "valang.blk"
#include "cbksrtbon1.blk"
#include "cbkchb.blk"
dimension rcore2(nsort),ecore2(nsort),acore2(nsort)
**********************************************************************
* *
* Read in force field *
@ -44,9 +45,6 @@ c$$$ write (65,*) 'In ffinpt'
c$$$ call timer(65)
c$$$ close (65)
c$$$ end if
open (4,file='ffield.reax',status='old')
rewind (4)
iline=0
read (4,'(a40)',end=990,err=990)qffield
@ -96,7 +94,7 @@ c$$$ end if
$bo131(i1),bo132(i1),bo133(i1),sigqeq(i1),default
iline=iline+1
read (4,1250,end=990,err=990)vovun(i1),vval1(i1),vrom,
$vval3(i1),vval4(i1)
$vval3(i1),vval4(i1),rcore2(i1),ecore2(i1),acore2(i1)
iline=iline+1
idef(i1)=int(default)
nphb(i1)=int(vnphb)
@ -108,6 +106,9 @@ c$$$ end if
**********************************************************************
do i1=1,nso
do i2=1,nso
rcore(i1,i2)=sqrt(rcore2(i1)*rcore2(i2))
ecore(i1,i2)=sqrt(ecore2(i1)*ecore2(i2))
acore(i1,i2)=sqrt(acore2(i1)*acore2(i2))
p1co(i1,i2)=sqrt(4.0*rvdw(i1)*rvdw(i2))
p2co(i1,i2)=sqrt(eps(i1)*eps(i2))
p3co(i1,i2)=sqrt(alf(i1)*alf(i2))
@ -261,6 +262,7 @@ c$$$ end if
990 write (*,*)'Error or end-of-file reading unit 4 on line:',iline
stop
999 continue
close(4)
**********************************************************************
* *
* Format part *
@ -2182,7 +2184,8 @@ c$$$ end if
$,end=40,err=40)
$ir,qlabel(na+1),qresi1(na+1),qresi2(na+1),qresi3(na+1),
$cglobal(na+1,1),cglobal(na+1,2),
$cglobal(na+1,3),qffty(na+1),ibgr1(na+1),ibgr2(na+1),chgbgf(na+1)
$cglobal(na+1,3),qffty(na+1),ibgr1(na+1),ibgr2(na+1),
$chgglobal(na+1)
else
stop 'Unsupported Biograf-version'
end if

2
lib/reax/reax_poten.F
View File

@ -2805,8 +2805,6 @@ c$$$ end if
exphuc=exp(-vpar(24)*boc)
bocor4=(1.0-exphua)*(1.0-exphub)*(1.0-exphuc)
eth=hsin*ethhulp*bocor4
estrain(j(2))=estrain(j(2))+0.50*eth
estrain(j(3))=estrain(j(3))+0.50*eth
detdar=hsin*bocor4*(0.50*v1(ity)-2.0*v2(ity)*bocor2*arg+
$v3(ity)*(6.0*arg2-1.5d0))

3
lib/reax/reax_reac.F
View File

@ -93,9 +93,10 @@ c$$$ end if
call lonpar
call covbon
call ovcor
call srtang !Determine valency angles
call srttor !Determine torsion angles
call srtoop !Determine out of plane angles
* call srtoop !Determine out of plane angles
call srthb !Determine hydrogen bonds
call calval