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fix uninitialized data access after restart bug in USER-YAFF pair styles 

also fix some source formatting issues
This commit is contained in:
Axel Kohlmeyer 2021-04-06 13:25:24 -04:00
parent db400c91ae
commit e01e0298cb
No known key found for this signature in database
GPG Key ID: D9B44E93BF0C375A
3 changed files with 31 additions and 27 deletions
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16
src/KSPACE/pair_lj_cut_coul_long.cpp
View File

@ -17,21 +17,21 @@
#include "pair_lj_cut_coul_long.h"
#include <cmath>
#include <cstring>
#include "atom.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "kspace.h"
#include "update.h"
#include "respa.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "neighbor.h"
#include "respa.h"
#include "update.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;

22
src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp
View File

@ -106,6 +106,7 @@ void PairLJSwitch3CoulGaussLong::compute(int eflag, int vflag)
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
@ -193,7 +194,7 @@ void PairLJSwitch3CoulGaussLong::compute(int eflag, int vflag)
offset[itype][jtype];
} else evdwl = 0.0;
// Truncation, see Yaff Switch33
// Truncation, see Yaff Switch3
if (truncw>0) {
if (rsq < cut_ljsq[itype][jtype]) {
if (r>cut_lj[itype][jtype]-truncw) {
@ -262,19 +263,18 @@ void PairLJSwitch3CoulGaussLong::allocate()
void PairLJSwitch3CoulGaussLong::settings(int narg, char **arg)
{
if (narg < 2 || narg > 3) error->all(FLERR,"Illegal pair_style command");
if (narg < 2 || narg > 3) error->all(FLERR,"Illegal pair_style command");
cut_lj_global = utils::numeric(FLERR,arg[0],false,lmp);
if (narg == 2) {
cut_coul = cut_lj_global;
truncw = utils::numeric(FLERR,arg[1],false,lmp);
}
else {
} else {
cut_coul = utils::numeric(FLERR,arg[1],false,lmp);
truncw = utils::numeric(FLERR,arg[2],false,lmp);
}
if (truncw>0.0) truncwi = 1.0/truncw;
else truncwi = 0.0;
// reset cutoffs that have been explicitly set
if (allocated) {
@ -332,6 +332,9 @@ void PairLJSwitch3CoulGaussLong::init_style()
cut_coulsq = cut_coul * cut_coul;
if (truncw>0.0) truncwi = 1.0/truncw;
else truncwi = 0.0;
// insure use of KSpace long-range solver, set g_ewald
if (force->kspace == nullptr)
@ -375,8 +378,7 @@ double PairLJSwitch3CoulGaussLong::init_one(int i, int j)
double r6inv = r2inv*r2inv*r2inv;
double r12inv = r6inv*r6inv;
offset[i][j] = lj3[i][j]*r12inv-lj4[i][j]*r6inv;
}
else {offset[i][j] = 0.0;}
} else {offset[i][j] = 0.0;}
} else offset[i][j] = 0.0;
cut_ljsq[j][i] = cut_ljsq[i][j];
@ -431,8 +433,7 @@ double PairLJSwitch3CoulGaussLong::init_one(int i, int j)
double t71 = -0.4e1 * cg * (0.2e1 * t10 * t11 - 0.2e1 * t10 * t14 + (cg5 - 0.2e1 * cg1) * t58 * cg5) * t26 / t4 / t41 / t9;
etail_ij = 2.0*MY_PI*all[0]*all[1]*t71;
ptail_ij = 2.0*MY_PI*all[0]*all[1]*t71;
}
else {
} else {
double t1 = pow(cg3, 0.2e1);
double t2 = t1 * t1;
double t3 = t2 * t1;
@ -618,6 +619,7 @@ double PairLJSwitch3CoulGaussLong::single(int i, int j, int itype, int jtype,
expn2 = 0.0;
erfc2 = 0.0;
forcecoul2 = 0.0;
prefactor2 = 0.0;
} else {
r = sqrt(rsq);
rrij = lj2[itype][jtype]*r;

20
src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp
View File

@ -106,6 +106,7 @@ void PairMM3Switch3CoulGaussLong::compute(int eflag, int vflag)
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
@ -170,6 +171,7 @@ void PairMM3Switch3CoulGaussLong::compute(int eflag, int vflag)
expn2 = 0.0;
erfc2 = 0.0;
forcecoul2 = 0.0;
prefactor2 = 0.0;
} else {
rrij = lj2[itype][jtype]*r;
expn2 = exp(-rrij*rrij);
@ -263,19 +265,18 @@ void PairMM3Switch3CoulGaussLong::allocate()
void PairMM3Switch3CoulGaussLong::settings(int narg, char **arg)
{
if (narg < 2 || narg > 3) error->all(FLERR,"Illegal pair_style command");
if (narg < 2 || narg > 3) error->all(FLERR,"Illegal pair_style command");
cut_lj_global = utils::numeric(FLERR,arg[0],false,lmp);
if (narg == 2) {
cut_coul = cut_lj_global;
truncw = utils::numeric(FLERR,arg[1],false,lmp);
}
else {
} else {
cut_coul = utils::numeric(FLERR,arg[1],false,lmp);
truncw = utils::numeric(FLERR,arg[2],false,lmp);
}
if (truncw>0.0) truncwi = 1.0/truncw;
else truncwi = 0.0;
// reset cutoffs that have been explicitly set
if (allocated) {
@ -333,6 +334,9 @@ void PairMM3Switch3CoulGaussLong::init_style()
cut_coulsq = cut_coul * cut_coul;
if (truncw>0.0) truncwi = 1.0/truncw;
else truncwi = 0.0;
// insure use of KSpace long-range solver, set g_ewald
if (force->kspace == nullptr)
@ -375,8 +379,7 @@ double PairMM3Switch3CoulGaussLong::init_one(int i, int j)
double r6inv = r2inv*r2inv*r2inv;
double expb = lj3[i][j]*exp(-lj1[i][j]*r);
offset[i][j] = expb-lj4[i][j]*r6inv;
}
else {offset[i][j] = 0.0;}
} else {offset[i][j] = 0.0;}
} else offset[i][j] = 0.0;
cut_ljsq[j][i] = cut_ljsq[i][j];
@ -426,8 +429,7 @@ double PairMM3Switch3CoulGaussLong::init_one(int i, int j)
double t64 = cg * (0.6388888889e3 * ((-t3 + (0.7e1 / 0.36e2 * cg5 - t5) * t1 - 0.2e1 / 0.3e1 * t8 * (cg5 - cg1 / 0.4e1) * cg3 + cg5 * t14) * t20 + t3 + (cg5 / 0.12e2 + t5) * t1 + (cg5 + cg1 / 0.3e1) * cg1 * cg3 / 0.2e1 + t30 * cg5) * t2 * t36 * t39 - 0.225e1 * (0.2e1 * t43 * t44 - 0.2e1 * t43 * t47 + cg5 * (cg5 - 0.2e1 * cg1)) * t54 * t1 / cg1 / t8 * t39);
etail_ij = 2.0*MY_PI*all[0]*all[1]*t64;
ptail_ij = 2.0*MY_PI*all[0]*all[1]*t64;
}
else {
} else {
double t2 = pow(cg3, 0.2e1);
double t3 = t2 * t2;
double t7 = 0.12e2 / cg3 * cg1;