From 6e225d90fc2926170176821e5ef1b8144bd38e3f Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 15 Nov 2018 16:48:38 -0500
Subject: [PATCH] fix some minor bugs write data file writing and remove dead
code and silence compiler warnings
---
src/USER-COLVARS/group_ndx.cpp | 4 ++--
src/USER-DPD/fix_rx.cpp | 6 ++++--
src/USER-MISC/compute_stress_mop_profile.cpp | 3 +--
src/USER-MOFFF/angle_class2_p6.cpp | 2 +-
src/USER-MOFFF/angle_cosine_buck6d.cpp | 2 +-
src/USER-MOFFF/improper_inversion_harmonic.cpp | 5 +++--
src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp | 2 +-
src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp | 2 +-
8 files changed, 14 insertions(+), 12 deletions(-)
diff --git a/src/USER-COLVARS/group_ndx.cpp b/src/USER-COLVARS/group_ndx.cpp
index 450c250ffa..858336c9d5 100644
--- a/src/USER-COLVARS/group_ndx.cpp
+++ b/src/USER-COLVARS/group_ndx.cpp
@@ -50,7 +50,7 @@ static int cmptagint(const void *p1, const void *p2)
static void write_group(FILE *fp, int gid, Atom *atom, Group *group, int me,
int np, MPI_Comm world, FILE *screen, FILE *logfile)
{
- char fmt[8];
+ char fmt[16];
tagint *sendlist, *recvlist;
bigint num = group->count(gid);
int lnum, cols;
@@ -73,7 +73,7 @@ static void write_group(FILE *fp, int gid, Atom *atom, Group *group, int me,
++i;
j /= 10;
}
- sprintf(fmt,"%%%dd ", i);
+ snprintf(fmt,16,"%%%dd ", i);
cols = 80 / (i+1);
}
diff --git a/src/USER-DPD/fix_rx.cpp b/src/USER-DPD/fix_rx.cpp
index 97668471c8..cb8349786f 100644
--- a/src/USER-DPD/fix_rx.cpp
+++ b/src/USER-DPD/fix_rx.cpp
@@ -758,8 +758,10 @@ void FixRX::pre_force(int /*vflag*/)
memory->create( diagnosticCounterPerODE[FuncSum], nlocal, "FixRX::diagnosticCounterPerODE");
}
- //#pragma omp parallel \
- // reduction(+: nSteps, nIters, nFuncs, nFails )
+#if 0
+ #pragma omp parallel \
+ reduction(+: nSteps, nIters, nFuncs, nFails )
+#endif
{
double *rwork = new double[8*nspecies];
diff --git a/src/USER-MISC/compute_stress_mop_profile.cpp b/src/USER-MISC/compute_stress_mop_profile.cpp
index 9189318381..76bf487630 100644
--- a/src/USER-MISC/compute_stress_mop_profile.cpp
+++ b/src/USER-MISC/compute_stress_mop_profile.cpp
@@ -451,10 +451,9 @@ void ComputeStressMopProfile::setup_bins()
int i,n;
double lo = 0.0, hi = 0.0;
- double *boxlo,*boxhi,*prd;
+ double *boxlo,*boxhi;
boxlo = domain->boxlo;
boxhi = domain->boxhi;
- prd = domain->prd;
if (originflag == LOWER) origin = boxlo[dir];
else if (originflag == UPPER) origin = boxhi[dir];
diff --git a/src/USER-MOFFF/angle_class2_p6.cpp b/src/USER-MOFFF/angle_class2_p6.cpp
index c821c9d883..d2a6e21e6b 100644
--- a/src/USER-MOFFF/angle_class2_p6.cpp
+++ b/src/USER-MOFFF/angle_class2_p6.cpp
@@ -429,7 +429,7 @@ void AngleClass2P6::read_restart(FILE *fp)
void AngleClass2P6::write_data(FILE *fp)
{
for (int i = 1; i <= atom->nangletypes; i++)
- fprintf(fp,"%d %g %g %g %g\n",
+ fprintf(fp,"%d %g %g %g %g %g %g\n",
i,theta0[i]/MY_PI*180.0,k2[i],k3[i],k4[i],k5[i],k6[i]);
fprintf(fp,"\nBondBond Coeffs\n\n");
diff --git a/src/USER-MOFFF/angle_cosine_buck6d.cpp b/src/USER-MOFFF/angle_cosine_buck6d.cpp
index 3f87aeb757..f358097802 100644
--- a/src/USER-MOFFF/angle_cosine_buck6d.cpp
+++ b/src/USER-MOFFF/angle_cosine_buck6d.cpp
@@ -353,7 +353,7 @@ void AngleCosineBuck6d::read_restart(FILE *fp)
void AngleCosineBuck6d::write_data(FILE *fp)
{
for (int i = 1; i <= atom->nangletypes; i++) {
- fprintf(fp,"%d %g %d %d\n",i,k[i],multiplicity[i],th0[i]);
+ fprintf(fp,"%d %g %d %g\n",i,k[i],multiplicity[i],th0[i]);
}
}
diff --git a/src/USER-MOFFF/improper_inversion_harmonic.cpp b/src/USER-MOFFF/improper_inversion_harmonic.cpp
index 9608d58054..8404984b53 100644
--- a/src/USER-MOFFF/improper_inversion_harmonic.cpp
+++ b/src/USER-MOFFF/improper_inversion_harmonic.cpp
@@ -241,8 +241,8 @@ void ImproperInversionHarmonic::invang(const int &i1,const int &i2,
f[i4][2] += f4[2];
}
- double rb3x, rb3y, rb3z;
- if (evflag)
+ if (evflag) {
+ double rb3x, rb3y, rb3z;
rb3x = vb1x - vb2x;
rb3y = vb1y - vb2y;
@@ -252,6 +252,7 @@ void ImproperInversionHarmonic::invang(const int &i1,const int &i2,
vb3x,vb3y,vb3z,
vb2x,vb2y,vb2z,
rb3x,rb3y,rb3z);
+ }
}
/* ---------------------------------------------------------------------- */
diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp b/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp
index f434d03858..46af95470c 100644
--- a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp
+++ b/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp
@@ -83,7 +83,7 @@ void PairBuck6dCoulGaussDSF::compute(int eflag, int vflag)
double r,rsq,r2inv,r6inv,r14inv,rexp,forcecoul,forcebuck6d,factor_coul,factor_lj;
double term1,term2,term3,term4,term5;
double rcu,rqu,sme,smf,ebuck6d;
- double prefactor,erfcc,erfcd,t,arg;
+ double prefactor,erfcc,erfcd,arg;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = ecoul = 0.0;
diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp b/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp
index 9902896d18..3c54d64770 100644
--- a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp
+++ b/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp
@@ -85,7 +85,7 @@ void PairBuck6dCoulGaussLong::compute(int eflag, int vflag)
double grij,expm2,erf;
double term1,term2,term3,term4,term5;
double rcu,rqu,sme,smf,ebuck6d,ealpha;
- double prefactor,erfa,expa,t,arg,falpha;
+ double prefactor,erfa,expa,arg,falpha;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = ecoul = 0.0;
--
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