Merge pull request #538 from akohlmey/collected-small-changes

Collected small changes and bugfixes
This commit is contained in:
sjplimp 2017-06-22 07:52:21 -06:00 committed by GitHub
commit 4fc3f4f7e5
147 changed files with 402 additions and 434 deletions

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@ -144,7 +144,11 @@ this fix.
"fix spring"_fix_spring.html, "fix adapt"_fix_adapt.html
[Restrictions:] none
[Restrictions:]
This fix is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Default:]

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

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@ -1337,8 +1337,8 @@ void PairLJLongTIP4PLong::compute_outer(int eflag, int vflag)
fH[1] = 0.5 * alpha * fd[1];
fH[2] = 0.5 * alpha * fd[2];
xH1 = x[jH1];
xH2 = x[jH2];
xH1 = x[iH1];
xH2 = x[iH2];
v[0] = x[i][0]*fO[0] + xH1[0]*fH[0] + xH2[0]*fH[0];
v[1] = x[i][1]*fO[1] + xH1[1]*fH[1] + xH2[1]*fH[1];
v[2] = x[i][2]*fO[2] + xH1[2]*fH[2] + xH2[2]*fH[2];

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@ -1271,7 +1271,7 @@ double PairAIREBO::bondorder(int i, int j, double rij[3],
double w21,dw21,r34[3],r34mag,cos234,w34,dw34;
double cross321[3],cross234[3],prefactor,SpN;
double fcijpc,fcikpc,fcjlpc,fcjkpc,fcilpc;
double dt2dik[3],dt2djl[3],dt2dij[3],aa,aaa1,aaa2,at2,cw,cwnum,cwnom;
double dt2dik[3],dt2djl[3],dt2dij[3],aa,aaa2,at2,cw,cwnum,cwnom;
double sin321,sin234,rr,rijrik,rijrjl,rjk2,rik2,ril2,rjl2;
double dctik,dctjk,dctjl,dctij,dctji,dctil,rik2i,rjl2i,sink2i,sinl2i;
double rjk[3],ril[3],dt1dik,dt1djk,dt1djl,dt1dil,dt1dij;
@ -1856,8 +1856,6 @@ double PairAIREBO::bondorder(int i, int j, double rij[3],
aa = (prefactor*2.0*cw/cwnom)*w21*w34 *
(1.0-tspjik)*(1.0-tspijl);
aaa1 = -prefactor*(1.0-square(om1234)) *
(1.0-tspjik)*(1.0-tspijl);
aaa2 = -prefactor*(1.0-square(om1234)) * w21*w34;
at2 = aa*cwnum;
@ -2107,7 +2105,7 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
double w21,dw21,r34[3],r34mag,cos234,w34,dw34;
double cross321[3],cross234[3],prefactor,SpN;
double fcikpc,fcjlpc,fcjkpc,fcilpc;
double dt2dik[3],dt2djl[3],aa,aaa1,aaa2,at2,cw,cwnum,cwnom;
double dt2dik[3],dt2djl[3],aa,aaa2,at2,cw,cwnum,cwnom;
double sin321,sin234,rr,rijrik,rijrjl,rjk2,rik2,ril2,rjl2;
double dctik,dctjk,dctjl,dctil,rik2i,rjl2i,sink2i,sinl2i;
double rjk[3],ril[3],dt1dik,dt1djk,dt1djl,dt1dil;
@ -2800,8 +2798,6 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
aa = (prefactor*2.0*cw/cwnom)*w21*w34 *
(1.0-tspjik)*(1.0-tspijl);
aaa1 = -prefactor*(1.0-square(om1234)) *
(1.0-tspjik)*(1.0-tspijl);
aaa2 = -prefactor*(1.0-square(om1234)) * w21*w34;
at2 = aa*cwnum;

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
Lammps - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
Lammps - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
Lammps - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

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@ -50,7 +50,7 @@ enum{NCOMMON};
ComputeCNPAtom::ComputeCNPAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
nearest(NULL), nnearest(NULL), cnpv(NULL)
list(NULL), nearest(NULL), nnearest(NULL), cnpv(NULL)
{
if (narg != 4) error->all(FLERR,"Illegal compute cnp/atom command");

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

View File

@ -1038,7 +1038,7 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag,
double w21,dw21,r34[3],r34mag,cos234,w34,dw34;
double cross321[3],cross234[3],prefactor,SpN;
double fcijpc,fcikpc,fcjlpc,fcjkpc,fcilpc;
double dt2dik[3],dt2djl[3],dt2dij[3],aa,aaa1,aaa2,at2,cw,cwnum,cwnom;
double dt2dik[3],dt2djl[3],dt2dij[3],aa,aaa2,at2,cw,cwnum,cwnom;
double sin321,sin234,rr,rijrik,rijrjl,rjk2,rik2,ril2,rjl2;
double dctik,dctjk,dctjl,dctij,dctji,dctil,rik2i,rjl2i,sink2i,sinl2i;
double rjk[3],ril[3],dt1dik,dt1djk,dt1djl,dt1dil,dt1dij;
@ -1628,8 +1628,6 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag,
aa = (prefactor*2.0*cw/cwnom)*w21*w34 *
(1.0-tspjik)*(1.0-tspijl);
aaa1 = -prefactor*(1.0-square(om1234)) *
(1.0-tspjik)*(1.0-tspijl);
aaa2 = -prefactor*(1.0-square(om1234)) * w21*w34;
at2 = aa*cwnum;
@ -1879,7 +1877,7 @@ double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double rij[3], double rijmag
double w21,dw21,r34[3],r34mag,cos234,w34,dw34;
double cross321[3],cross234[3],prefactor,SpN;
double fcikpc,fcjlpc,fcjkpc,fcilpc;
double dt2dik[3],dt2djl[3],aa,aaa1,aaa2,at2,cw,cwnum,cwnom;
double dt2dik[3],dt2djl[3],aa,aaa2,at2,cw,cwnum,cwnom;
double sin321,sin234,rr,rijrik,rijrjl,rjk2,rik2,ril2,rjl2;
double dctik,dctjk,dctjl,dctil,rik2i,rjl2i,sink2i,sinl2i;
double rjk[3],ril[3],dt1dik,dt1djk,dt1djl,dt1dil;
@ -2572,8 +2570,6 @@ double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double rij[3], double rijmag
aa = (prefactor*2.0*cw/cwnom)*w21*w34 *
(1.0-tspjik)*(1.0-tspijl);
aaa1 = -prefactor*(1.0-square(om1234)) *
(1.0-tspjik)*(1.0-tspijl);
aaa2 = -prefactor*(1.0-square(om1234)) * w21*w34;
at2 = aa*cwnum;

View File

@ -572,17 +572,18 @@ void PairReaxCOMP::read_reax_forces(int vflag)
void PairReaxCOMP::FindBond()
{
int i, ii, j, pj, jtag, nj, jtmp, jj;
double bo_tmp, bo_cut, rij, rsq;
bond_data *bo_ij;
bo_cut = 0.10;
const double bo_cut = 0.10;
int i;
#if defined(_OPENMP)
#pragma omp parallel for schedule(static) default(shared) \
private(i, nj, pj, bo_ij, j, bo_tmp)
private(i)
#endif
for (i = 0; i < system->n; i++) {
int j, pj, nj;
double bo_tmp;
bond_data *bo_ij;
nj = 0;
for( pj = Start_Index(i, lists); pj < End_Index(i, lists); ++pj ) {
bo_ij = &( lists->select.bond_list[pj] );

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

View File

@ -55,7 +55,6 @@ void Add_dBond_to_ForcesOMP( reax_system *system, int i, int pj,
long reductionOffset = (system->N * tid);
/* Virial Tallying variables */
double f_scaler;
rvec fi_tmp, fj_tmp, fk_tmp, delij, delji, delki, delkj, temp;
/* Initializations */
@ -229,14 +228,11 @@ void Add_dBond_to_Forces_NPTOMP( reax_system *system, int i, int pj, simulation_
ivec rel_box;
int pk, k, j;
PairReaxCOMP *pair_reax_ptr = static_cast<class PairReaxCOMP*>(system->pair_ptr);
#if defined(_OPENMP)
int tid = omp_get_thread_num();
#else
int tid = 0;
#endif
ThrData *thr = pair_reax_ptr->getFixOMP()->get_thr(tid);
long reductionOffset = (system->N * tid);
/* Initializations */
@ -430,12 +426,9 @@ void BOOMP( reax_system *system, control_params *control, simulation_data *data,
#endif
double p_lp1 = system->reax_param.gp.l[15];
int num_bonds = 0;
double p_boc1 = system->reax_param.gp.l[0];
double p_boc2 = system->reax_param.gp.l[1];
reax_list *bonds = (*lists) + BONDS;
int natoms = system->N;
int nthreads = control->nthreads;
#if defined(_OPENMP)
#pragma omp parallel default(shared)
@ -454,11 +447,6 @@ void BOOMP( reax_system *system, control_params *control, simulation_data *data,
two_body_parameters *twbp;
bond_order_data *bo_ij, *bo_ji;
#if defined(_OPENMP)
int tid = omp_get_thread_num();
#else
int tid = 0;
#endif
/* Calculate Deltaprime, Deltaprime_boc values */
#if defined(_OPENMP)
#pragma omp for schedule(static)

View File

@ -49,14 +49,13 @@ void BondsOMP( reax_system *system, control_params *control,
startTimeBase = MPI_Wtime();
#endif
int natoms = system->n;
int nthreads = control->nthreads;
const int natoms = system->n;
reax_list *bonds = (*lists) + BONDS;
double gp3 = system->reax_param.gp.l[3];
double gp4 = system->reax_param.gp.l[4];
double gp7 = system->reax_param.gp.l[7];
double gp10 = system->reax_param.gp.l[10];
double gp37 = (int) system->reax_param.gp.l[37];
const double gp3 = system->reax_param.gp.l[3];
const double gp4 = system->reax_param.gp.l[4];
const double gp7 = system->reax_param.gp.l[7];
const double gp10 = system->reax_param.gp.l[10];
const int gp37 = (int) system->reax_param.gp.l[37];
double total_Ebond = 0.0;
#if defined(_OPENMP)
@ -66,9 +65,8 @@ void BondsOMP( reax_system *system, control_params *control,
int i, j, pj;
int start_i, end_i;
int type_i, type_j;
double ebond, ebond_thr=0.0, pow_BOs_be2, exp_be12, CEbo;
double gp3, gp4, gp7, gp10, gp37;
double exphu, exphua1, exphub1, exphuov, hulpov, estriph, estriph_thr=0.0;
double ebond, pow_BOs_be2, exp_be12, CEbo;
double exphu, exphua1, exphub1, exphuov, hulpov, estriph;
double decobdbo, decobdboua, decobdboub;
single_body_parameters *sbp_i, *sbp_j;
two_body_parameters *twbp;

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@ -265,7 +265,6 @@ void Validate_ListsOMP( reax_system *system, storage *workspace, reax_list **lis
{
int i, comp, Hindex;
reax_list *bonds, *hbonds;
reallocate_data *realloc = &(workspace->realloc);
double saferzone = system->saferzone;
#if defined(_OPENMP)
@ -335,25 +334,21 @@ void Init_Forces_noQEq_OMP( reax_system *system, control_params *control,
startTimeBase = MPI_Wtime();
#endif
int i, j, pi, pj;
int start_i, end_i, start_j, end_j;
int i, j, pj;
int start_i, end_i;
int type_i, type_j;
int ihb, jhb, ihb_top, jhb_top;
int local, flag;
double r_ij, cutoff;
double cutoff;
single_body_parameters *sbp_i, *sbp_j;
two_body_parameters *twbp;
far_neighbor_data *nbr_pj;
reax_atom *atom_i, *atom_j;
bond_data *ibond, *jbond;
reax_list *far_nbrs = *lists + FAR_NBRS;
reax_list *bonds = *lists + BONDS;
reax_list *hbonds = *lists + HBONDS;
int num_bonds = 0;
int num_hbonds = 0;
int btop_i = 0;
int btop_j = 0;
int renbr = (data->step-data->prev_steps) % control->reneighbor == 0;
// We will use CdDeltaReduction as a temporary (double) buffer to accumulate total_bond_order
// This is safe because CdDeltaReduction is currently zeroed and its accumulation doesn't start until BondsOMP()
@ -368,8 +363,8 @@ void Init_Forces_noQEq_OMP( reax_system *system, control_params *control,
#if defined(_OPENMP)
#pragma omp parallel default(shared) \
private(i, atom_i, type_i, pi, start_i, end_i, sbp_i, btop_i, ibond, ihb, ihb_top, \
j, atom_j, type_j, pj, start_j, end_j, sbp_j, nbr_pj, jbond, jhb, twbp)
private(i, atom_i, type_i, start_i, end_i, sbp_i, btop_i, ihb, ihb_top, \
j, atom_j, type_j, pj, sbp_j, nbr_pj, jhb, twbp)
#endif
{
@ -417,7 +412,6 @@ void Init_Forces_noQEq_OMP( reax_system *system, control_params *control,
// outside of critical section.
// Start top portion of BOp()
int jj = nbr_pj->nbr;
double C12, C34, C56;
double BO, BO_s, BO_pi, BO_pi2;
double bo_cut = control->bo_cut;
@ -602,7 +596,6 @@ void Compute_ForcesOMP( reax_system *system, control_params *control,
reax_list **lists, output_controls *out_control,
mpi_datatypes *mpi_data )
{
int qeq_flag;
MPI_Comm comm = mpi_data->world;
// Init Forces

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@ -50,16 +50,14 @@ void Atom_EnergyOMP( reax_system *system, control_params *control,
#endif
/* Initialize parameters */
double p_lp1 = system->reax_param.gp.l[15];
double p_lp3 = system->reax_param.gp.l[5];
double p_ovun3 = system->reax_param.gp.l[32];
double p_ovun4 = system->reax_param.gp.l[31];
double p_ovun6 = system->reax_param.gp.l[6];
double p_ovun7 = system->reax_param.gp.l[8];
double p_ovun8 = system->reax_param.gp.l[9];
const double p_lp3 = system->reax_param.gp.l[5];
const double p_ovun3 = system->reax_param.gp.l[32];
const double p_ovun4 = system->reax_param.gp.l[31];
const double p_ovun6 = system->reax_param.gp.l[6];
const double p_ovun7 = system->reax_param.gp.l[8];
const double p_ovun8 = system->reax_param.gp.l[9];
int natoms = system->n;
int nthreads = control->nthreads;
const int natoms = system->n;
reax_list *bonds = (*lists) + BONDS;
double total_Elp = 0.0;
@ -79,11 +77,11 @@ void Atom_EnergyOMP( reax_system *system, control_params *control,
double exp_ovun2n, exp_ovun6, exp_ovun8;
double inv_exp_ovun1, inv_exp_ovun2, inv_exp_ovun2n, inv_exp_ovun8;
double e_un, CEunder1, CEunder2, CEunder3, CEunder4;
double eng_tmp, f_tmp;
double eng_tmp;
double p_lp2, p_ovun2, p_ovun5;
int numbonds;
single_body_parameters *sbp_i, *sbp_j;
single_body_parameters *sbp_i;
two_body_parameters *twbp;
bond_data *pbond;
bond_order_data *bo_ij;

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@ -48,8 +48,6 @@ void vdW_Coulomb_Energy_OMP( reax_system *system, control_params *control,
reax_list **lists, output_controls *out_control ) {
int natoms = system->n;
int nthreads = control->nthreads;
long totalReductionSize = system->N * nthreads;
reax_list *far_nbrs = (*lists) + FAR_NBRS;
double p_vdW1 = system->reax_param.gp.l[28];
double p_vdW1i = 1.0 / p_vdW1;
@ -71,7 +69,8 @@ void vdW_Coulomb_Energy_OMP( reax_system *system, control_params *control,
double tmp, r_ij, fn13, exp1, exp2;
double Tap, dTap, dfn13, CEvd, CEclmb, de_core;
double dr3gamij_1, dr3gamij_3;
double e_ele, e_ele_thr, e_vdW, e_vdW_thr, e_core, SMALL = 0.0001;
double e_ele, e_vdW, e_core;
const double SMALL = 0.0001;
double e_lg, de_lg, r_ij5, r_ij6, re6;
rvec temp, ext_press;
two_body_parameters *twbp;
@ -92,7 +91,6 @@ void vdW_Coulomb_Energy_OMP( reax_system *system, control_params *control,
system->pair_ptr->vatom, thr);
e_core = 0;
e_vdW = 0;
e_vdW_thr = 0;
e_lg = 0;
de_lg = 0.0;
@ -263,8 +261,6 @@ void Tabulated_vdW_Coulomb_Energy_OMP(reax_system *system,control_params *contro
double SMALL = 0.0001;
int natoms = system->n;
reax_list *far_nbrs = (*lists) + FAR_NBRS;
int nthreads = control->nthreads;
long totalReductionSize = system->N * nthreads;
double total_EvdW = 0.;
double total_Eele = 0.;

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

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@ -514,8 +514,6 @@ void FixReaxCSpecies::FindMolecule ()
int *ilist;
double bo_tmp,bo_cut;
double **spec_atom = f_SPECBOND->array_atom;
const double * const * const x = atom->x;
const int nlocal = atom->nlocal;
inum = reaxc->list->inum;
ilist = reaxc->list->ilist;

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*

View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*

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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*

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