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remove dead code and reduce compiler warnings

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# Conflicts:
#	src/RIGID/fix_rigid_small.cpp
This commit is contained in:
Axel Kohlmeyer
2022-02-10 14:41:09 -05:00
parent 44ded1c1fe
commit 6366972ef4
15 changed files with 28 additions and 161 deletions
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5
src/CG-DNA/pair_oxdna2_dh.cpp
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@ -18,7 +18,6 @@
#include "pair_oxdna2_dh.h"
#include "atom.h"
#include "atom_vec_ellipsoid.h"
#include "comm.h"
#include "error.h"
#include "force.h"
@ -101,10 +100,6 @@ void PairOxdna2Dh::compute(int eflag, int vflag)
int *alist,*blist,*numneigh,**firstneigh;
double *special_lj = force->special_lj;
AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
int *ellipsoid = atom->ellipsoid;
int a,b,ia,ib,anum,bnum,atype,btype;
evdwl = 0.0;

13
src/CG-DNA/pair_oxdna_coaxstk.cpp
View File

@ -18,7 +18,6 @@
#include "pair_oxdna_coaxstk.h"
#include "atom.h"
#include "atom_vec_ellipsoid.h"
#include "comm.h"
#include "error.h"
#include "force.h"
@ -107,7 +106,7 @@ PairOxdnaCoaxstk::~PairOxdnaCoaxstk()
void PairOxdnaCoaxstk::compute(int eflag, int vflag)
{
double delf[3],delt[3],delta[3],deltb[3]; // force, torque increment;
double evdwl,fpair,finc,tpair,factor_lj;
double evdwl,finc,tpair,factor_lj;
double v1tmp[3],v2tmp[3],v3tmp[3];
double delr_ss[3],delr_ss_norm[3],rsq_ss,r_ss,rinv_ss;
double delr_st[3],delr_st_norm[3],rsq_st,r_st,rinv_st;
@ -142,10 +141,6 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag)
int *alist,*blist,*numneigh,**firstneigh;
double *special_lj = force->special_lj;
AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
int *ellipsoid = atom->ellipsoid;
int a,b,ia,ib,anum,bnum,atype,btype;
double f2,f4t1,f4t4,f4t5,f4t6,f5c3;
@ -345,8 +340,6 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag)
// force, torque and virial contribution for forces between stacking sites
fpair = 0.0;
delf[0] = 0.0;
delf[1] = 0.0;
delf[2] = 0.0;
@ -361,7 +354,6 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag)
// radial force
finc = -df2 * f4t1 * f4t4 * f4t5 * f4t6 * f5c3 * f5c3 * rinv_st * factor_lj;
fpair += finc;
delf[0] += delr_st[0] * finc;
delf[1] += delr_st[1] * finc;
@ -371,7 +363,6 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag)
if (theta5 && theta5p) {
finc = -f2 * f4t1 * f4t4 * df4t5 * f4t6 * f5c3 * f5c3 * rinv_st * factor_lj;
fpair += finc;
delf[0] += (delr_st_norm[0]*cost5 - az[0]) * finc;
delf[1] += (delr_st_norm[1]*cost5 - az[1]) * finc;
@ -383,7 +374,6 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag)
if (theta6 && theta6p) {
finc = -f2 * f4t1* f4t4 * f4t5 * df4t6 * f5c3 * f5c3 * rinv_st * factor_lj;
fpair += finc;
delf[0] += (delr_st_norm[0]*cost6 - bz[0]) * finc;
delf[1] += (delr_st_norm[1]*cost6 - bz[1]) * finc;
@ -400,7 +390,6 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag)
ay[2] = ny_xtrct[a][2];
finc = -f2 * f4t1* f4t4 * f4t5 * f4t6 * 2.0 * f5c3 * df5c3 * factor_lj;
fpair += finc;
gamma = d_cs - d_cst;
gammacub = gamma * gamma * gamma;

4
src/CG-DNA/pair_oxdna_excv.h
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@ -41,8 +41,8 @@ class PairOxdnaExcv : public Pair {
void write_data(FILE *) override;
void write_data_all(FILE *) override;
void *extract(const char *, int &) override;
virtual int pack_forward_comm(int, int *, double *, int, int *);
virtual void unpack_forward_comm(int, int, double *);
int pack_forward_comm(int, int *, double *, int, int *) override;
void unpack_forward_comm(int, int, double *) override;
protected:
// s=sugar-phosphate backbone site, b=base site, st=stacking site

14
src/CG-DNA/pair_oxdna_hbond.cpp
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@ -18,7 +18,6 @@
#include "pair_oxdna_hbond.h"
#include "atom.h"
#include "atom_vec_ellipsoid.h"
#include "comm.h"
#include "error.h"
#include "force.h"
@ -135,7 +134,7 @@ void PairOxdnaHbond::compute(int eflag, int vflag)
{
double delf[3],delta[3],deltb[3]; // force, torque increment;
double evdwl,fpair,finc,tpair,factor_lj;
double evdwl,finc,tpair,factor_lj;
double delr_hb[3],delr_hb_norm[3],rsq_hb,r_hb,rinv_hb;
double theta1,t1dir[3],cost1;
double theta2,t2dir[3],cost2;
@ -162,10 +161,6 @@ void PairOxdnaHbond::compute(int eflag, int vflag)
int *alist,*blist,*numneigh,**firstneigh;
double *special_lj = force->special_lj;
AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
int *ellipsoid = atom->ellipsoid;
int a,b,ia,ib,anum,bnum,atype,btype;
double f1,f4t1,f4t4,f4t2,f4t3,f4t7,f4t8;
@ -338,8 +333,6 @@ void PairOxdnaHbond::compute(int eflag, int vflag)
// force, torque and virial contribution for forces between h-bonding sites
fpair = 0.0;
delf[0] = 0.0;
delf[1] = 0.0;
delf[2] = 0.0;
@ -354,7 +347,6 @@ void PairOxdnaHbond::compute(int eflag, int vflag)
// radial force
finc = -df1 * f4t1 * f4t2 * f4t3 * f4t4 * f4t7 * f4t8 * factor_lj;
fpair += finc;
delf[0] += delr_hb[0] * finc;
delf[1] += delr_hb[1] * finc;
@ -364,7 +356,6 @@ void PairOxdnaHbond::compute(int eflag, int vflag)
if (theta2) {
finc = -f1 * f4t1 * df4t2 * f4t3 * f4t4 * f4t7 * f4t8 * rinv_hb * factor_lj;
fpair += finc;
delf[0] += (delr_hb_norm[0]*cost2 + ax[0]) * finc;
delf[1] += (delr_hb_norm[1]*cost2 + ax[1]) * finc;
@ -376,7 +367,6 @@ void PairOxdnaHbond::compute(int eflag, int vflag)
if (theta3) {
finc = -f1 * f4t1 * f4t2 * df4t3 * f4t4 * f4t7 * f4t8 * rinv_hb * factor_lj;
fpair += finc;
delf[0] += (delr_hb_norm[0]*cost3 - bx[0]) * finc;
delf[1] += (delr_hb_norm[1]*cost3 - bx[1]) * finc;
@ -388,7 +378,6 @@ void PairOxdnaHbond::compute(int eflag, int vflag)
if (theta7) {
finc = -f1 * f4t1 * f4t2 * f4t3 * f4t4 * df4t7 * f4t8 * rinv_hb * factor_lj;
fpair += finc;
delf[0] += (delr_hb_norm[0]*cost7 + az[0]) * finc;
delf[1] += (delr_hb_norm[1]*cost7 + az[1]) * finc;
@ -400,7 +389,6 @@ void PairOxdnaHbond::compute(int eflag, int vflag)
if (theta8) {
finc = -f1 * f4t1 * f4t2 * f4t3 * f4t4 * f4t7 * df4t8 * rinv_hb * factor_lj;
fpair += finc;
delf[0] += (delr_hb_norm[0]*cost8 - bz[0]) * finc;
delf[1] += (delr_hb_norm[1]*cost8 - bz[1]) * finc;

16
src/CG-DNA/pair_oxdna_stk.cpp
View File

@ -18,7 +18,6 @@
#include "pair_oxdna_stk.h"
#include "atom.h"
#include "atom_vec_ellipsoid.h"
#include "comm.h"
#include "error.h"
#include "force.h"
@ -213,7 +212,7 @@ void PairOxdnaStk::ev_tally_xyz(int i, int j, int nlocal, int newton_bond,
void PairOxdnaStk::compute(int eflag, int vflag)
{
double delf[3],delta[3],deltb[3]; // force, torque increment;
double evdwl,fpair,finc,tpair;
double evdwl,finc,tpair;
double delr_ss[3],delr_ss_norm[3],rsq_ss,r_ss,rinv_ss;
double delr_st[3],delr_st_norm[3],rsq_st,r_st,rinv_st;
double theta4,t4dir[3],cost4;
@ -243,10 +242,6 @@ void PairOxdnaStk::compute(int eflag, int vflag)
tagint *id5p = atom->id5p;
AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
int *ellipsoid = atom->ellipsoid;
int a,b,btemp,in,atype,btype;
double f1,f4t4,f4t5,f4t6,f5c1,f5c2;
@ -430,8 +425,6 @@ void PairOxdnaStk::compute(int eflag, int vflag)
// force, torque and virial contribution for forces between stacking sites
fpair = 0.0;
delf[0] = 0.0;
delf[1] = 0.0;
delf[2] = 0.0;
@ -446,7 +439,6 @@ void PairOxdnaStk::compute(int eflag, int vflag)
// radial force
finc = -df1 * f4t4 * f4t5 * f4t6 * f5c1 * f5c2;
fpair += finc;
delf[0] += delr_st[0] * finc;
delf[1] += delr_st[1] * finc;
@ -456,7 +448,6 @@ void PairOxdnaStk::compute(int eflag, int vflag)
if (theta5p) {
finc = -f1 * f4t4 * df4t5 * f4t6 * f5c1 * f5c2 * rinv_st;
fpair += finc;
delf[0] += (delr_st_norm[0]*cost5p - bz[0]) * finc;
delf[1] += (delr_st_norm[1]*cost5p - bz[1]) * finc;
@ -468,7 +459,6 @@ void PairOxdnaStk::compute(int eflag, int vflag)
if (theta6p) {
finc = -f1 * f4t4 * f4t5 * df4t6 * f5c1 * f5c2 * rinv_st;
fpair += finc;
delf[0] += (delr_st_norm[0]*cost6p - az[0]) * finc;
delf[1] += (delr_st_norm[1]*cost6p - az[1]) * finc;
@ -520,8 +510,6 @@ void PairOxdnaStk::compute(int eflag, int vflag)
// force, torque and virial contribution for forces between backbone sites
fpair = 0.0;
delf[0] = 0.0;
delf[1] = 0.0;
delf[2] = 0.0;
@ -538,7 +526,6 @@ void PairOxdnaStk::compute(int eflag, int vflag)
if (cosphi1) {
finc = -f1 * f4t4 * f4t5 * f4t6 * df5c1 * f5c2 * rinv_ss;
fpair += finc;
delf[0] += (delr_ss_norm[0]*cosphi1 - by[0]) * finc;
delf[1] += (delr_ss_norm[1]*cosphi1 - by[1]) * finc;
@ -550,7 +537,6 @@ void PairOxdnaStk::compute(int eflag, int vflag)
if (cosphi2) {
finc = -f1 * f4t4 * f4t5 * f4t6 * f5c1 * df5c2 * rinv_ss;
fpair += finc;
delf[0] += (delr_ss_norm[0]*cosphi2 - ay[0]) * finc;
delf[1] += (delr_ss_norm[1]*cosphi2 - ay[1]) * finc;

14
src/CG-DNA/pair_oxdna_xstk.cpp
View File

@ -18,7 +18,6 @@
#include "pair_oxdna_xstk.h"
#include "atom.h"
#include "atom_vec_ellipsoid.h"
#include "comm.h"
#include "error.h"
#include "force.h"
@ -112,7 +111,7 @@ PairOxdnaXstk::~PairOxdnaXstk()
void PairOxdnaXstk::compute(int eflag, int vflag)
{
double delf[3],delta[3],deltb[3]; // force, torque increment;
double evdwl,fpair,finc,tpair,factor_lj;
double evdwl,finc,tpair,factor_lj;
double delr_hb[3],delr_hb_norm[3],rsq_hb,r_hb,rinv_hb;
double theta1,t1dir[3],cost1;
double theta2,t2dir[3],cost2;
@ -139,10 +138,6 @@ void PairOxdnaXstk::compute(int eflag, int vflag)
int *alist,*blist,*numneigh,**firstneigh;
double *special_lj = force->special_lj;
AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
int *ellipsoid = atom->ellipsoid;
int a,b,ia,ib,anum,bnum,atype,btype;
double f2,f4t1,f4t4,f4t2,f4t3,f4t7,f4t8;
@ -337,8 +332,6 @@ void PairOxdnaXstk::compute(int eflag, int vflag)
// force, torque and virial contribution for forces between h-bonding sites
fpair = 0.0;
delf[0] = 0.0;
delf[1] = 0.0;
delf[2] = 0.0;
@ -353,7 +346,6 @@ void PairOxdnaXstk::compute(int eflag, int vflag)
// radial force
finc = -df2 * f4t1 * f4t2 * f4t3 * f4t4 * f4t7 * f4t8 * rinv_hb *factor_lj;
fpair += finc;
delf[0] += delr_hb[0] * finc;
delf[1] += delr_hb[1] * finc;
@ -363,7 +355,6 @@ void PairOxdnaXstk::compute(int eflag, int vflag)
if (theta2) {
finc = -f2 * f4t1 * df4t2 * f4t3 * f4t4 * f4t7 * f4t8 * rinv_hb * factor_lj;
fpair += finc;
delf[0] += (delr_hb_norm[0]*cost2 + ax[0]) * finc;
delf[1] += (delr_hb_norm[1]*cost2 + ax[1]) * finc;
@ -375,7 +366,6 @@ void PairOxdnaXstk::compute(int eflag, int vflag)
if (theta3) {
finc = -f2 * f4t1 * f4t2 * df4t3 * f4t4 * f4t7 * f4t8 * rinv_hb * factor_lj;
fpair += finc;
delf[0] += (delr_hb_norm[0]*cost3 - bx[0]) * finc;
delf[1] += (delr_hb_norm[1]*cost3 - bx[1]) * finc;
@ -387,7 +377,6 @@ void PairOxdnaXstk::compute(int eflag, int vflag)
if (theta7) {
finc = -f2 * f4t1 * f4t2 * f4t3 * f4t4 * df4t7 * f4t8 * rinv_hb * factor_lj;
fpair += finc;
delf[0] += (delr_hb_norm[0]*cost7 + az[0]) * finc;
delf[1] += (delr_hb_norm[1]*cost7 + az[1]) * finc;
@ -399,7 +388,6 @@ void PairOxdnaXstk::compute(int eflag, int vflag)
if (theta8) {
finc = -f2 * f4t1 * f4t2 * f4t3 * f4t4 * f4t7 * df4t8 * rinv_hb * factor_lj;
fpair += finc;
delf[0] += (delr_hb_norm[0]*cost8 - bz[0]) * finc;
delf[1] += (delr_hb_norm[1]*cost8 - bz[1]) * finc;

18
src/CG-DNA/pair_oxrna2_stk.cpp
View File

@ -18,7 +18,6 @@
#include "pair_oxrna2_stk.h"
#include "atom.h"
#include "atom_vec_ellipsoid.h"
#include "comm.h"
#include "error.h"
#include "force.h"
@ -222,7 +221,7 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
{
double delf[3],delta[3],deltb[3]; // force, torque increment;
double evdwl,fpair,finc,tpair;
double evdwl,finc,tpair;
double delr_ss[3],delr_ss_norm[3],rsq_ss,r_ss,rinv_ss;
double delr_st[3],delr_st_norm[3],rsq_st,r_st,rinv_st;
double theta5p,t5pdir[3],cost5p;
@ -262,10 +261,6 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
tagint *id5p = atom->id5p;
AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
int *ellipsoid = atom->ellipsoid;
int a,b,btemp,in,atype,btype;
double f1,f4t5,f4t6,f4t9,f4t10,f5c1,f5c2;
@ -462,8 +457,6 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
// force, torque and virial contribution for forces between stacking sites
fpair = 0.0;
delf[0] = 0.0;
delf[1] = 0.0;
delf[2] = 0.0;
@ -478,7 +471,6 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
// radial force
finc = -df1 * f4t5 * f4t6 * f4t9 * f4t10 * f5c1 * f5c2;
fpair += finc;
delf[0] += delr_st[0] * finc;
delf[1] += delr_st[1] * finc;
@ -488,7 +480,6 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
if (theta5p) {
finc = -f1 * df4t5 * f4t6 * f4t9 * f4t10 * f5c1 * f5c2 * rinv_st;
fpair += finc;
delf[0] += (delr_st_norm[0]*cost5p - bz[0]) * finc;
delf[1] += (delr_st_norm[1]*cost5p - bz[1]) * finc;
@ -500,7 +491,6 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
if (theta6p) {
finc = -f1 * f4t5 * df4t6 * f4t9 * f4t10 * f5c1 * f5c2 * rinv_st;
fpair += finc;
delf[0] += (delr_st_norm[0]*cost6p - az[0]) * finc;
delf[1] += (delr_st_norm[1]*cost6p - az[1]) * finc;
@ -552,8 +542,6 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
// force, torque and virial contribution for forces between backbone sites
fpair = 0.0;
delf[0] = 0.0;
delf[1] = 0.0;
delf[2] = 0.0;
@ -570,7 +558,6 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
if (theta9) {
finc = -f1 * f4t5 * f4t6 * df4t9 * f4t10 * f5c1 * f5c2 * rinv_ss;
fpair += finc;
delf[0] += (delr_ss_norm[0]*cost9 - aux3p[0]) * finc;
delf[1] += (delr_ss_norm[1]*cost9 - aux3p[1]) * finc;
@ -582,7 +569,6 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
if (theta10) {
finc = -f1 * f4t5 * f4t6 * f4t9 * df4t10 * f5c1 * f5c2 * rinv_ss;
fpair += finc;
delf[0] += (delr_ss_norm[0]*cost10 - aux5p[0]) * finc;
delf[1] += (delr_ss_norm[1]*cost10 - aux5p[1]) * finc;
@ -594,7 +580,6 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
if (cosphi1) {
finc = -f1 * f4t5 * f4t6 * f4t9 * f4t10 * df5c1 * f5c2 * rinv_ss;
fpair += finc;
delf[0] += (delr_ss_norm[0]*cosphi1 - by[0]) * finc;
delf[1] += (delr_ss_norm[1]*cosphi1 - by[1]) * finc;
@ -606,7 +591,6 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
if (cosphi2) {
finc = -f1 * f4t5 * f4t6 * f4t9 * f4t10 * f5c1 * df5c2 * rinv_ss;
fpair += finc;
delf[0] += (delr_ss_norm[0]*cosphi2 - ay[0]) * finc;
delf[1] += (delr_ss_norm[1]*cosphi2 - ay[1]) * finc;

14
src/CG-DNA/pair_oxrna2_xstk.cpp
View File

@ -18,7 +18,6 @@
#include "pair_oxrna2_xstk.h"
#include "atom.h"
#include "atom_vec_ellipsoid.h"
#include "comm.h"
#include "error.h"
#include "force.h"
@ -107,7 +106,7 @@ void PairOxrna2Xstk::compute(int eflag, int vflag)
{
double delf[3],delta[3],deltb[3]; // force, torque increment;
double evdwl,fpair,finc,tpair,factor_lj;
double evdwl,finc,tpair,factor_lj;
double delr_hb[3],delr_hb_norm[3],rsq_hb,r_hb,rinv_hb;
double theta1,t1dir[3],cost1;
double theta2,t2dir[3],cost2;
@ -134,10 +133,6 @@ void PairOxrna2Xstk::compute(int eflag, int vflag)
int *alist,*blist,*numneigh,**firstneigh;
double *special_lj = force->special_lj;
AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
int *ellipsoid = atom->ellipsoid;
int a,b,ia,ib,anum,bnum,atype,btype;
double f2,f4t1,f4t2,f4t3,f4t7,f4t8;
@ -310,8 +305,6 @@ void PairOxrna2Xstk::compute(int eflag, int vflag)
// force, torque and virial contribution for forces between h-bonding sites
fpair = 0.0;
delf[0] = 0.0;
delf[1] = 0.0;
delf[2] = 0.0;
@ -326,7 +319,6 @@ void PairOxrna2Xstk::compute(int eflag, int vflag)
// radial force
finc = -df2 * f4t1 * f4t2 * f4t3 * f4t7 * f4t8 * rinv_hb *factor_lj;
fpair += finc;
delf[0] += delr_hb[0] * finc;
delf[1] += delr_hb[1] * finc;
@ -336,7 +328,6 @@ void PairOxrna2Xstk::compute(int eflag, int vflag)
if (theta2) {
finc = -f2 * f4t1 * df4t2 * f4t3 * f4t7 * f4t8 * rinv_hb * factor_lj;
fpair += finc;
delf[0] += (delr_hb_norm[0]*cost2 + ax[0]) * finc;
delf[1] += (delr_hb_norm[1]*cost2 + ax[1]) * finc;
@ -348,7 +339,6 @@ void PairOxrna2Xstk::compute(int eflag, int vflag)
if (theta3) {
finc = -f2 * f4t1 * f4t2 * df4t3 * f4t7 * f4t8 * rinv_hb * factor_lj;
fpair += finc;
delf[0] += (delr_hb_norm[0]*cost3 - bx[0]) * finc;
delf[1] += (delr_hb_norm[1]*cost3 - bx[1]) * finc;
@ -360,7 +350,6 @@ void PairOxrna2Xstk::compute(int eflag, int vflag)
if (theta7) {
finc = -f2 * f4t1 * f4t2 * f4t3 * df4t7 * f4t8 * rinv_hb * factor_lj;
fpair += finc;
delf[0] += (delr_hb_norm[0]*cost7 + az[0]) * finc;
delf[1] += (delr_hb_norm[1]*cost7 + az[1]) * finc;
@ -372,7 +361,6 @@ void PairOxrna2Xstk::compute(int eflag, int vflag)
if (theta8) {
finc = -f2 * f4t1 * f4t2 * f4t3 * f4t7 * df4t8 * rinv_hb * factor_lj;
fpair += finc;
delf[0] += (delr_hb_norm[0]*cost8 - bz[0]) * finc;
delf[1] += (delr_hb_norm[1]*cost8 - bz[1]) * finc;

16
src/DPD-REACT/fix_rx.cpp
View File

@ -689,20 +689,14 @@ void FixRX::pre_force(int /*vflag*/)
// Zero the counters for the ODE solvers.
int nSteps = 0;
int nIters = 0;
int nFuncs = 0;
int nFails = 0;
if (odeIntegrationFlag == ODE_LAMMPS_RKF45 && diagnosticFrequency == 1)
{
if (odeIntegrationFlag == ODE_LAMMPS_RKF45 && diagnosticFrequency == 1) {
memory->create( diagnosticCounterPerODE[StepSum], nlocal, "FixRX::diagnosticCounterPerODE");
memory->create( diagnosticCounterPerODE[FuncSum], nlocal, "FixRX::diagnosticCounterPerODE");
}
#if 0
#pragma omp parallel \
reduction(+: nSteps, nIters, nFuncs, nFails )
#endif
{
double *rwork = new double[8*nspecies];
@ -712,11 +706,8 @@ void FixRX::pre_force(int /*vflag*/)
int ode_counter[4] = { 0 };
//#pragma omp for schedule(runtime)
for (int i = 0; i < nlocal; i++)
{
if (mask[i] & groupbit)
{
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
double theta;
if (localTempFlag)
theta = dpdThetaLocal[i];
@ -735,7 +726,6 @@ void FixRX::pre_force(int /*vflag*/)
}
nSteps += ode_counter[0];
nIters += ode_counter[1];
nFuncs += ode_counter[2];
nFails += ode_counter[3];

2
src/EXTRA-PAIR/pair_harmonic_cut.cpp
View File

@ -146,7 +146,7 @@ void PairHarmonicCut::allocate()
global settings
------------------------------------------------------------------------- */
void PairHarmonicCut::settings(int narg, char **arg)
void PairHarmonicCut::settings(int narg, char ** /*arg*/)
{
if (narg > 0) error->all(FLERR, "Illegal pair_style command");
}

16
src/GRANULAR/pair_gran_hertz_history.cpp
View File

@ -204,11 +204,12 @@ void PairGranHertzHistory::compute(int eflag, int vflag)
shrmag = sqrt(shear[0]*shear[0] + shear[1]*shear[1] +
shear[2]*shear[2]);
// rotate shear displacements
rsht = shear[0]*delx + shear[1]*dely + shear[2]*delz;
rsht *= rsqinv;
if (shearupdate) {
// rotate shear displacements
rsht = shear[0]*delx + shear[1]*dely + shear[2]*delz;
rsht *= rsqinv;
shear[0] -= rsht*delx;
shear[1] -= rsht*dely;
shear[2] -= rsht*delz;
@ -320,7 +321,7 @@ double PairGranHertzHistory::single(int i, int j, int /*itype*/, int /*jtype*/,
double r,rinv,rsqinv,delx,dely,delz;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3,wr1,wr2,wr3;
double mi,mj,meff,damp,ccel,polyhertz;
double vtr1,vtr2,vtr3,vrel,shrmag,rsht;
double vtr1,vtr2,vtr3,vrel,shrmag;
double fs1,fs2,fs3,fs,fn;
double *radius = atom->radius;
@ -426,11 +427,6 @@ double PairGranHertzHistory::single(int i, int j, int /*itype*/, int /*jtype*/,
shrmag = sqrt(shear[0]*shear[0] + shear[1]*shear[1] +
shear[2]*shear[2]);
// rotate shear displacements
rsht = shear[0]*delx + shear[1]*dely + shear[2]*delz;
rsht *= rsqinv;
// tangential forces = shear + tangential velocity damping
fs1 = -polyhertz * (kt*shear[0] + meff*gammat*vtr1);

16
src/GRANULAR/pair_gran_hooke_history.cpp
View File

@ -264,11 +264,12 @@ void PairGranHookeHistory::compute(int eflag, int vflag)
}
shrmag = sqrt(shear[0] * shear[0] + shear[1] * shear[1] + shear[2] * shear[2]);
// rotate shear displacements
rsht = shear[0] * delx + shear[1] * dely + shear[2] * delz;
rsht *= rsqinv;
if (shearupdate) {
// rotate shear displacements
rsht = shear[0] * delx + shear[1] * dely + shear[2] * delz;
rsht *= rsqinv;
shear[0] -= rsht * delx;
shear[1] -= rsht * dely;
shear[2] -= rsht * delz;
@ -616,7 +617,7 @@ double PairGranHookeHistory::single(int i, int j, int /*itype*/, int /*jtype*/,
double r, rinv, rsqinv, delx, dely, delz;
double vr1, vr2, vr3, vnnr, vn1, vn2, vn3, vt1, vt2, vt3, wr1, wr2, wr3;
double mi, mj, meff, damp, ccel;
double vtr1, vtr2, vtr3, vrel, shrmag, rsht;
double vtr1, vtr2, vtr3, vrel, shrmag;
double fs1, fs2, fs3, fs, fn;
double *radius = atom->radius;
@ -718,11 +719,6 @@ double PairGranHookeHistory::single(int i, int j, int /*itype*/, int /*jtype*/,
double *shear = &allshear[3 * neighprev];
shrmag = sqrt(shear[0] * shear[0] + shear[1] * shear[1] + shear[2] * shear[2]);
// rotate shear displacements
rsht = shear[0] * delx + shear[1] * dely + shear[2] * delz;
rsht *= rsqinv;
// tangential forces = shear + tangential velocity damping
fs1 = -(kt * shear[0] + meff * gammat * vtr1);

16
src/OPENMP/pair_reaxff_omp.cpp
View File

@ -226,7 +226,6 @@ void PairReaxFFOMP::setup()
void PairReaxFFOMP::compute(int eflag, int vflag)
{
double evdwl,ecoul;
// communicate num_bonds once every reneighboring
// 2 num arrays stored by fix, grab ptr to them
@ -235,7 +234,6 @@ void PairReaxFFOMP::compute(int eflag, int vflag)
int *num_bonds = fix_reaxff->num_bonds;
int *num_hbonds = fix_reaxff->num_hbonds;
evdwl = ecoul = 0.0;
ev_init(eflag,vflag);
api->system->n = atom->nlocal; // my atoms
@ -304,20 +302,6 @@ void PairReaxFFOMP::compute(int eflag, int vflag)
// energies and pressure
if (eflag_global) {
evdwl += api->data->my_en.e_bond;
evdwl += api->data->my_en.e_ov;
evdwl += api->data->my_en.e_un;
evdwl += api->data->my_en.e_lp;
evdwl += api->data->my_en.e_ang;
evdwl += api->data->my_en.e_pen;
evdwl += api->data->my_en.e_coa;
evdwl += api->data->my_en.e_hb;
evdwl += api->data->my_en.e_tor;
evdwl += api->data->my_en.e_con;
evdwl += api->data->my_en.e_vdW;
ecoul += api->data->my_en.e_ele;
ecoul += api->data->my_en.e_pol;
// Store the different parts of the energy
// in a list for output by compute pair command

17
src/REAXFF/pair_reaxff.cpp
View File

@ -455,8 +455,6 @@ double PairReaxFF::init_one(int i, int j)
void PairReaxFF::compute(int eflag, int vflag)
{
double evdwl,ecoul;
// communicate num_bonds once every reneighboring
// 2 num arrays stored by fix, grab ptr to them
@ -464,7 +462,6 @@ void PairReaxFF::compute(int eflag, int vflag)
int *num_bonds = fix_reaxff->num_bonds;
int *num_hbonds = fix_reaxff->num_hbonds;
evdwl = ecoul = 0.0;
ev_init(eflag,vflag);
api->system->n = atom->nlocal; // my atoms
@ -496,20 +493,6 @@ void PairReaxFF::compute(int eflag, int vflag)
// energies and pressure
if (eflag_global) {
evdwl += api->data->my_en.e_bond;
evdwl += api->data->my_en.e_ov;
evdwl += api->data->my_en.e_un;
evdwl += api->data->my_en.e_lp;
evdwl += api->data->my_en.e_ang;
evdwl += api->data->my_en.e_pen;
evdwl += api->data->my_en.e_coa;
evdwl += api->data->my_en.e_hb;
evdwl += api->data->my_en.e_tor;
evdwl += api->data->my_en.e_con;
evdwl += api->data->my_en.e_vdW;
ecoul += api->data->my_en.e_ele;
ecoul += api->data->my_en.e_pol;
// Store the different parts of the energy
// in a list for output by compute pair command

8
src/RIGID/fix_rigid_small.cpp
View File

@ -1351,8 +1351,8 @@ void FixRigidSmall::set_xv()
vr[4] = 0.5*x0*fc2;
vr[5] = 0.5*x1*fc2;
double rlist[][3] = {{x0, x1, x2}};
double flist[][3] = {{0.5*fc0, 0.5*fc1, 0.5*fc2}};
double rlist[1][3] = {{x0, x1, x2}};
double flist[1][3] = {{0.5*fc0, 0.5*fc1, 0.5*fc2}};
v_tally(1,&i,1.0,vr,rlist,flist,b->xgc);
}
}
@ -1513,8 +1513,8 @@ void FixRigidSmall::set_v()
vr[4] = 0.5*x0*fc2;
vr[5] = 0.5*x1*fc2;
double rlist[][3] = {{x0, x1, x2}};
double flist[][3] = {{0.5*fc0, 0.5*fc1, 0.5*fc2}};
double rlist[1][3] = {{x0, x1, x2}};
double flist[1][3] = {{0.5*fc0, 0.5*fc1, 0.5*fc2}};
v_tally(1,&i,1.0,vr,rlist,flist,b->xgc);
}
}