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Merge pull request #2666 from akohlmey/collected-small-changes

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Collected small changes and fixes
This commit is contained in:
Axel Kohlmeyer
2021-03-19 13:32:42 -04:00
committed by GitHub
parent 0dd32d2f99 154b8cb401
commit 41c2a82ccc
66 changed files with 154 additions and 331 deletions
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7
cmake/Modules/Packages/USER-INTEL.cmake
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@ -30,7 +30,12 @@ if(INTEL_LRT_MODE STREQUAL "THREADS")
endif()
endif()
if(INTEL_LRT_MODE STREQUAL "C++11")
target_compile_definitions(lammps PRIVATE -DLMP_INTEL_USELRT -DLMP_INTEL_LRT11)
if(Threads_FOUND)
target_compile_definitions(lammps PRIVATE -DLMP_INTEL_USELRT -DLMP_INTEL_LRT11)
target_link_libraries(lammps PRIVATE Threads::Threads)
else()
message(FATAL_ERROR "Must have working threads library for Long-range thread support")
endif()
endif()
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")

2
src/MC/fix_gcmc.cpp
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@ -2330,7 +2330,9 @@ double FixGCMC::energy_full()
// unlike Verlet, not performing a reverse_comm() or forces here
// b/c GCMC does not care about forces
// don't think it will mess up energy due to any post_force() fixes
// but Modify::pre_reverse() is needed for USER-INTEL
if (modify->n_pre_reverse) modify->pre_reverse(eflag,vflag);
if (modify->n_post_force) modify->post_force(vflag);
if (modify->n_end_of_step) modify->end_of_step();

2
src/MC/fix_widom.cpp
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@ -1057,7 +1057,9 @@ double FixWidom::energy_full()
// unlike Verlet, not performing a reverse_comm() or forces here
// b/c Widom does not care about forces
// don't think it will mess up energy due to any post_force() fixes
// but Modify::pre_reverse() is needed for USER-INTEL
if (modify->n_pre_reverse) modify->pre_reverse(eflag,vflag);
if (modify->n_pre_force) modify->pre_force(vflag);
if (modify->n_end_of_step) modify->end_of_step();

8
src/USER-OMP/pair_comb_omp.cpp
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@ -88,7 +88,7 @@ void PairCombOMP::eval(int iifrom, int iito, ThrData * const thr)
int i,j,k,ii,jj,kk,jnum,iparam_i;
tagint itag,jtag;
int itype,jtype,ktype,iparam_ij,iparam_ijk;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,rsq1,rsq2;
double delr1[3],delr2[3],fi[3],fj[3],fk[3];
double zeta_ij,prefactor;
@ -102,7 +102,7 @@ void PairCombOMP::eval(int iifrom, int iito, ThrData * const thr)
double vionij,fvionij,sr1,sr2,sr3,Eov,Fov;
int sht_jnum, *sht_jlist, nj;
evdwl = ecoul = 0.0;
evdwl = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
@ -419,7 +419,7 @@ double PairCombOMP::yasu_char(double *qf_fix, int &igroup)
#pragma omp parallel for private(ii) LMP_DEFAULT_NONE LMP_SHARED(potal,fac11e)
#endif
for (ii = 0; ii < inum; ii ++) {
double fqi,fqj,fqij,fqji,fqjj,delr1[3];
double fqi,fqij,fqji,fqjj,delr1[3];
double sr1,sr2,sr3;
int mr1,mr2,mr3;
@ -428,7 +428,7 @@ double PairCombOMP::yasu_char(double *qf_fix, int &igroup)
int nj = 0;
if (mask[i] & groupbit) {
fqi = fqj = fqij = fqji = fqjj = 0.0; // should not be needed.
fqi = fqij = fqji = fqjj = 0.0; // should not be needed.
int itype = map[type[i]];
const double xtmp = x[i][0];
const double ytmp = x[i][1];

15
src/compute.cpp
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@ -49,22 +49,15 @@ Compute::Compute(LAMMPS *lmp, int narg, char **arg) :
// compute ID, group, and style
// ID must be all alphanumeric chars or underscores
int n = strlen(arg[0]) + 1;
id = new char[n];
strcpy(id,arg[0]);
for (int i = 0; i < n-1; i++)
if (!isalnum(id[i]) && id[i] != '_')
error->all(FLERR,
"Compute ID must be alphanumeric or underscore characters");
id = utils::strdup(arg[0]);
if (!utils::is_id(id))
error->all(FLERR,"Compute ID must be alphanumeric or underscore characters");
igroup = group->find(arg[1]);
if (igroup == -1) error->all(FLERR,"Could not find compute group ID");
groupbit = group->bitmask[igroup];
n = strlen(arg[2]) + 1;
style = new char[n];
strcpy(style,arg[2]);
style = utils::strdup(arg[2]);
// set child class defaults

8
src/compute_angle_local.cpp
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@ -67,9 +67,7 @@ ComputeAngleLocal::ComputeAngleLocal(LAMMPS *lmp, int narg, char **arg) :
bstyle[nvalues++] = ENG;
} else if (strncmp(arg[iarg],"v_",2) == 0) {
bstyle[nvalues++] = VARIABLE;
int n = strlen(arg[iarg]);
vstr[nvar] = new char[n];
strcpy(vstr[nvar],&arg[iarg][2]);
vstr[nvar] = utils::strdup(&arg[iarg][2]);
nvar++;
} else break;
}
@ -85,9 +83,7 @@ ComputeAngleLocal::ComputeAngleLocal(LAMMPS *lmp, int narg, char **arg) :
if (iarg+3 > narg) error->all(FLERR,"Illegal compute angle/local command");
if (strcmp(arg[iarg+1],"theta") == 0) {
delete [] tstr;
int n = strlen(arg[iarg+2]) + 1;
tstr = new char[n];
strcpy(tstr,arg[iarg+2]);
tstr = utils::strdup(arg[iarg+2]);
tflag = 1;
} else error->all(FLERR,"Illegal compute angle/local command");
iarg += 3;

4
src/compute_angmom_chunk.cpp
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@ -41,9 +41,7 @@ ComputeAngmomChunk::ComputeAngmomChunk(LAMMPS *lmp, int narg, char **arg) :
// ID of compute chunk/atom
int n = strlen(arg[3]) + 1;
idchunk = new char[n];
strcpy(idchunk,arg[3]);
idchunk = utils::strdup(arg[3]);
init();

8
src/compute_bond_local.cpp
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@ -74,9 +74,7 @@ ComputeBondLocal::ComputeBondLocal(LAMMPS *lmp, int narg, char **arg) :
else if (strcmp(arg[iarg],"velvib") == 0) bstyle[nvalues++] = VELVIB;
else if (strncmp(arg[iarg],"v_",2) == 0) {
bstyle[nvalues++] = VARIABLE;
int n = strlen(arg[iarg]);
vstr[nvar] = new char[n];
strcpy(vstr[nvar],&arg[iarg][2]);
vstr[nvar] = utils::strdup(&arg[iarg][2]);
nvar++;
} else break;
}
@ -92,9 +90,7 @@ ComputeBondLocal::ComputeBondLocal(LAMMPS *lmp, int narg, char **arg) :
if (iarg+3 > narg) error->all(FLERR,"Illegal compute bond/local command");
if (strcmp(arg[iarg+1],"dist") == 0) {
delete [] dstr;
int n = strlen(arg[iarg+2]) + 1;
dstr = new char[n];
strcpy(dstr,arg[iarg+2]);
dstr = utils::strdup(arg[iarg+2]);
} else error->all(FLERR,"Illegal compute bond/local command");
iarg += 3;
} else error->all(FLERR,"Illegal compute bond/local command");

4
src/compute_centroid_stress_atom.cpp
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@ -51,9 +51,7 @@ ComputeCentroidStressAtom::ComputeCentroidStressAtom(LAMMPS *lmp, int narg, char
if (strcmp(arg[3],"NULL") == 0) id_temp = nullptr;
else {
int n = strlen(arg[3]) + 1;
id_temp = new char[n];
strcpy(id_temp,arg[3]);
id_temp = utils::strdup(arg[3]);
int icompute = modify->find_compute(id_temp);
if (icompute < 0)

4
src/compute_chunk_atom.cpp
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@ -185,9 +185,7 @@ ComputeChunkAtom::ComputeChunkAtom(LAMMPS *lmp, int narg, char **arg) :
int iregion = domain->find_region(arg[iarg+1]);
if (iregion == -1)
error->all(FLERR,"Region ID for compute chunk/atom does not exist");
int n = strlen(arg[iarg+1]) + 1;
idregion = new char[n];
strcpy(idregion,arg[iarg+1]);
idregion = utils::strdup(arg[iarg+1]);
regionflag = 1;
iarg += 2;
} else if (strcmp(arg[iarg],"nchunk") == 0) {

4
src/compute_chunk_spread_atom.cpp
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@ -36,9 +36,7 @@ ComputeChunkSpreadAtom(LAMMPS *lmp, int narg, char **arg) :
// ID of compute chunk/atom
int n = strlen(arg[3]) + 1;
idchunk = new char[n];
strcpy(idchunk,arg[3]);
idchunk = utils::strdup(arg[3]);
init_chunk();
// expand args if any have wildcard character "*"

4
src/compute_com_chunk.cpp
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@ -43,9 +43,7 @@ ComputeCOMChunk::ComputeCOMChunk(LAMMPS *lmp, int narg, char **arg) :
// ID of compute chunk/atom
int n = strlen(arg[3]) + 1;
idchunk = new char[n];
strcpy(idchunk,arg[3]);
idchunk = utils::strdup(arg[3]);
init();

4
src/compute_coord_atom.cpp
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@ -85,9 +85,7 @@ ComputeCoordAtom::ComputeCoordAtom(LAMMPS *lmp, int narg, char **arg) :
cstyle = ORIENT;
if (narg != 6) error->all(FLERR,"Illegal compute coord/atom command");
int n = strlen(arg[4]) + 1;
id_orientorder = new char[n];
strcpy(id_orientorder,arg[4]);
id_orientorder = utils::strdup(arg[4]);
int iorientorder = modify->find_compute(id_orientorder);
if (iorientorder < 0)

8
src/compute_dihedral_local.cpp
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@ -64,9 +64,7 @@ ComputeDihedralLocal::ComputeDihedralLocal(LAMMPS *lmp, int narg, char **arg) :
bstyle[nvalues++] = PHI;
} else if (strncmp(arg[iarg],"v_",2) == 0) {
bstyle[nvalues++] = VARIABLE;
int n = strlen(arg[iarg]);
vstr[nvar] = new char[n];
strcpy(vstr[nvar],&arg[iarg][2]);
vstr[nvar] = utils::strdup(&arg[iarg][2]);
nvar++;
} else break;
}
@ -83,9 +81,7 @@ ComputeDihedralLocal::ComputeDihedralLocal(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Illegal compute dihedral/local command");
if (strcmp(arg[iarg+1],"phi") == 0) {
delete [] pstr;
int n = strlen(arg[iarg+2]) + 1;
pstr = new char[n];
strcpy(pstr,arg[iarg+2]);
pstr = utils::strdup(arg[iarg+2]);
} else error->all(FLERR,"Illegal compute dihedral/local command");
iarg += 3;
} else error->all(FLERR,"Illegal compute dihedral/local command");

4
src/compute_dipole_chunk.cpp
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@ -49,9 +49,7 @@ ComputeDipoleChunk::ComputeDipoleChunk(LAMMPS *lmp, int narg, char **arg) :
// ID of compute chunk/atom
int n = strlen(arg[3]) + 1;
idchunk = new char[n];
strcpy(idchunk,arg[3]);
idchunk = utils::strdup(arg[3]);
usecenter = MASSCENTER;

12
src/compute_displace_atom.cpp
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@ -53,9 +53,7 @@ ComputeDisplaceAtom::ComputeDisplaceAtom(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Illegal compute displace/atom command");
refreshflag = 1;
delete [] rvar;
int n = strlen(arg[iarg+1]) + 1;
rvar = new char[n];
strcpy(rvar,arg[iarg+1]);
rvar = utils::strdup(arg[iarg+1]);
iarg += 2;
} else error->all(FLERR,"Illegal compute displace/atom command");
}
@ -74,11 +72,9 @@ ComputeDisplaceAtom::ComputeDisplaceAtom(LAMMPS *lmp, int narg, char **arg) :
// create a new fix STORE style
// id = compute-ID + COMPUTE_STORE, fix group = compute group
std::string cmd = id + std::string("_COMPUTE_STORE");
id_fix = new char[cmd.size()+1];
strcpy(id_fix,cmd.c_str());
cmd += fmt::format(" {} STORE peratom 1 3", group->names[igroup]);
id_fix = utils::strdup(std::string(id) + "_COMPUTE_STORE");
std::string cmd = id_fix + fmt::format(" {} STORE peratom 1 3",
group->names[igroup]);
modify->add_fix(cmd);
fix = (FixStore *) modify->fix[modify->nfix-1];

5
src/compute_group_group.cpp
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@ -54,10 +54,7 @@ ComputeGroupGroup::ComputeGroupGroup(LAMMPS *lmp, int narg, char **arg) :
extscalar = 1;
extvector = 1;
int n = strlen(arg[3]) + 1;
group2 = new char[n];
strcpy(group2,arg[3]);
group2 = utils::strdup(arg[3]);
jgroup = group->find(group2);
if (jgroup == -1)
error->all(FLERR,"Compute group/group group ID does not exist");

4
src/compute_gyration_chunk.cpp
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@ -36,9 +36,7 @@ ComputeGyrationChunk::ComputeGyrationChunk(LAMMPS *lmp, int narg, char **arg) :
// ID of compute chunk/atom
int n = strlen(arg[3]) + 1;
idchunk = new char[n];
strcpy(idchunk,arg[3]);
idchunk = utils::strdup(arg[3]);
init();

14
src/compute_heat_flux.cpp
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@ -43,17 +43,9 @@ ComputeHeatFlux::ComputeHeatFlux(LAMMPS *lmp, int narg, char **arg) :
// store ke/atom, pe/atom, stress/atom IDs used by heat flux computation
// insure they are valid for these computations
int n = strlen(arg[3]) + 1;
id_ke = new char[n];
strcpy(id_ke,arg[3]);
n = strlen(arg[4]) + 1;
id_pe = new char[n];
strcpy(id_pe,arg[4]);
n = strlen(arg[5]) + 1;
id_stress = new char[n];
strcpy(id_stress,arg[5]);
id_ke = utils::strdup(arg[3]);
id_pe = utils::strdup(arg[4]);
id_stress = utils::strdup(arg[5]);
int ike = modify->find_compute(id_ke);
int ipe = modify->find_compute(id_pe);

4
src/compute_inertia_chunk.cpp
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@ -41,9 +41,7 @@ ComputeInertiaChunk::ComputeInertiaChunk(LAMMPS *lmp, int narg, char **arg) :
// ID of compute chunk/atom
int n = strlen(arg[3]) + 1;
idchunk = new char[n];
strcpy(idchunk,arg[3]);
idchunk = utils::strdup(arg[3]);
init();

12
src/compute_msd_chunk.cpp
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@ -44,9 +44,7 @@ ComputeMSDChunk::ComputeMSDChunk(LAMMPS *lmp, int narg, char **arg) :
// ID of compute chunk/atom
int n = strlen(arg[3]) + 1;
idchunk = new char[n];
strcpy(idchunk,arg[3]);
idchunk = utils::strdup(arg[3]);
firstflag = 1;
init();
@ -58,11 +56,9 @@ ComputeMSDChunk::ComputeMSDChunk(LAMMPS *lmp, int narg, char **arg) :
// potentially re-populate the fix array (and change it to correct size)
// otherwise size reset and init will be done in setup()
std::string fixcmd = id + std::string("_COMPUTE_STORE");
id_fix = new char[fixcmd.size()+1];
strcpy(id_fix,fixcmd.c_str());
fixcmd += fmt::format(" {} STORE global 1 1",group->names[igroup]);
id_fix = utils::strdup(std::string(id) + "_COMPUTE_STORE");
std::string fixcmd = id_fix
+ fmt::format(" {} STORE global 1 1",group->names[igroup]);
modify->add_fix(fixcmd);
fix = (FixStore *) modify->fix[modify->nfix-1];
}

4
src/compute_omega_chunk.cpp
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@ -45,9 +45,7 @@ ComputeOmegaChunk::ComputeOmegaChunk(LAMMPS *lmp, int narg, char **arg) :
// ID of compute chunk/atom
int n = strlen(arg[3]) + 1;
idchunk = new char[n];
strcpy(idchunk,arg[3]);
idchunk = utils::strdup(arg[3]);
init();

11
src/compute_pair.cpp
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@ -37,10 +37,10 @@ ComputePair::ComputePair(LAMMPS *lmp, int narg, char **arg) :
peflag = 1;
timeflag = 1;
int n = strlen(arg[3]) + 1;
if (lmp->suffix) n += strlen(lmp->suffix) + 1;
pstyle = new char[n];
strcpy(pstyle,arg[3]);
// copy with suffix so we can later chop it off, if needed
if (lmp->suffix)
pstyle = utils::strdup(fmt::format("{}/{}",arg[3],lmp->suffix));
else pstyle = utils::strdup(arg[3]);
int iarg = 4;
nsub = 0;
@ -67,8 +67,7 @@ ComputePair::ComputePair(LAMMPS *lmp, int narg, char **arg) :
pair = force->pair_match(pstyle,1,nsub);
if (!pair && lmp->suffix) {
strcat(pstyle,"/");
strcat(pstyle,lmp->suffix);
pstyle[strlen(pstyle) - strlen(lmp->suffix) - 1] = '\0';
pair = force->pair_match(pstyle,1,nsub);
}

15
src/compute_pressure.cpp
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@ -53,9 +53,7 @@ ComputePressure::ComputePressure(LAMMPS *lmp, int narg, char **arg) :
if (strcmp(arg[3],"NULL") == 0) id_temp = nullptr;
else {
int n = strlen(arg[3]) + 1;
id_temp = new char[n];
strcpy(id_temp,arg[3]);
id_temp = utils::strdup(arg[3]);
int icompute = modify->find_compute(id_temp);
if (icompute < 0)
@ -82,10 +80,10 @@ ComputePressure::ComputePressure(LAMMPS *lmp, int narg, char **arg) :
while (iarg < narg) {
if (strcmp(arg[iarg],"ke") == 0) keflag = 1;
else if (strcmp(arg[iarg],"pair/hybrid") == 0) {
int n = strlen(arg[++iarg]) + 1;
if (lmp->suffix) n += strlen(lmp->suffix) + 1;
pstyle = new char[n];
strcpy(pstyle,arg[iarg++]);
if (lmp->suffix)
pstyle = utils::strdup(fmt::format("{}/{}",arg[++iarg],lmp->suffix));
else
pstyle = utils::strdup(arg[++iarg]);
nsub = 0;
@ -102,8 +100,7 @@ ComputePressure::ComputePressure(LAMMPS *lmp, int narg, char **arg) :
pairhybrid = (Pair *) force->pair_match(pstyle,1,nsub);
if (!pairhybrid && lmp->suffix) {
strcat(pstyle,"/");
strcat(pstyle,lmp->suffix);
pstyle[strlen(pstyle) - strlen(lmp->suffix) - 1] = '\0';
pairhybrid = (Pair *) force->pair_match(pstyle,1,nsub);
}

4
src/compute_property_chunk.cpp
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@ -33,9 +33,7 @@ ComputePropertyChunk::ComputePropertyChunk(LAMMPS *lmp, int narg, char **arg) :
// ID of compute chunk/atom
int n = strlen(arg[3]) + 1;
idchunk = new char[n];
strcpy(idchunk,arg[3]);
idchunk = utils::strdup(arg[3]);
init();

4
src/compute_reduce.cpp
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@ -47,9 +47,7 @@ ComputeReduce::ComputeReduce(LAMMPS *lmp, int narg, char **arg) :
iregion = domain->find_region(arg[3]);
if (iregion == -1)
error->all(FLERR,"Region ID for compute reduce/region does not exist");
int n = strlen(arg[3]) + 1;
idregion = new char[n];
strcpy(idregion,arg[3]);
idregion = utils::strdup(arg[3]);
iarg = 4;
}

4
src/compute_reduce_chunk.cpp
View File

@ -45,9 +45,7 @@ ComputeReduceChunk::ComputeReduceChunk(LAMMPS *lmp, int narg, char **arg) :
// ID of compute chunk/atom
int n = strlen(arg[3]) + 1;
idchunk = new char[n];
strcpy(idchunk,arg[3]);
idchunk = utils::strdup(arg[3]);
init_chunk();
// mode

4
src/compute_stress_atom.cpp
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@ -51,9 +51,7 @@ ComputeStressAtom::ComputeStressAtom(LAMMPS *lmp, int narg, char **arg) :
if (strcmp(arg[3],"NULL") == 0) id_temp = nullptr;
else {
int n = strlen(arg[3]) + 1;
id_temp = new char[n];
strcpy(id_temp,arg[3]);
id_temp = utils::strdup(arg[3]);
int icompute = modify->find_compute(id_temp);
if (icompute < 0)

8
src/compute_temp_chunk.cpp
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@ -44,9 +44,7 @@ ComputeTempChunk::ComputeTempChunk(LAMMPS *lmp, int narg, char **arg) :
// ID of compute chunk/atom
int n = strlen(arg[3]) + 1;
idchunk = new char[n];
strcpy(idchunk,arg[3]);
idchunk = utils::strdup(arg[3]);
biasflag = 0;
init();
@ -87,9 +85,7 @@ ComputeTempChunk::ComputeTempChunk(LAMMPS *lmp, int narg, char **arg) :
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute temp/chunk command");
biasflag = 1;
int n = strlen(arg[iarg+1]) + 1;
id_bias = new char[n];
strcpy(id_bias,arg[iarg+1]);
id_bias = utils::strdup(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"adof") == 0) {
if (iarg+2 > narg)

4
src/compute_temp_region.cpp
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@ -36,9 +36,7 @@ ComputeTempRegion::ComputeTempRegion(LAMMPS *lmp, int narg, char **arg) :
iregion = domain->find_region(arg[3]);
if (iregion == -1)
error->all(FLERR,"Region ID for compute temp/region does not exist");
int n = strlen(arg[3]) + 1;
idregion = new char[n];
strcpy(idregion,arg[3]);
idregion = utils::strdup(arg[3]);
scalar_flag = vector_flag = 1;
size_vector = 6;

4
src/compute_temp_sphere.cpp
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@ -51,9 +51,7 @@ ComputeTempSphere::ComputeTempSphere(LAMMPS *lmp, int narg, char **arg) :
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute temp/sphere command");
tempbias = 1;
int n = strlen(arg[iarg+1]) + 1;
id_bias = new char[n];
strcpy(id_bias,arg[iarg+1]);
id_bias = utils::strdup(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"dof") == 0) {
if (iarg+2 > narg)

4
src/compute_torque_chunk.cpp
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@ -40,9 +40,7 @@ ComputeTorqueChunk::ComputeTorqueChunk(LAMMPS *lmp, int narg, char **arg) :
// ID of compute chunk/atom
int n = strlen(arg[3]) + 1;
idchunk = new char[n];
strcpy(idchunk,arg[3]);
idchunk = utils::strdup(arg[3]);
init();

4
src/compute_vcm_chunk.cpp
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@ -41,9 +41,7 @@ ComputeVCMChunk::ComputeVCMChunk(LAMMPS *lmp, int narg, char **arg) :
// ID of compute chunk/atom
int n = strlen(arg[3]) + 1;
idchunk = new char[n];
strcpy(idchunk,arg[3]);
idchunk = utils::strdup(arg[3]);
init();

14
src/fix.cpp
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@ -42,21 +42,15 @@ Fix::Fix(LAMMPS *lmp, int /*narg*/, char **arg) :
// fix ID, group, and style
// ID must be all alphanumeric chars or underscores
int n = strlen(arg[0]) + 1;
id = new char[n];
strcpy(id,arg[0]);
for (int i = 0; i < n-1; i++)
if (!isalnum(id[i]) && id[i] != '_')
error->all(FLERR,"Fix ID must be alphanumeric or underscore characters");
id = utils::strdup(arg[0]);
if (!utils::is_id(id))
error->all(FLERR,"Fix ID must be alphanumeric or underscore characters");
igroup = group->find(arg[1]);
if (igroup == -1) error->all(FLERR,"Could not find fix group ID");
groupbit = group->bitmask[igroup];
n = strlen(arg[2]) + 1;
style = new char[n];
strcpy(style,arg[2]);
style = utils::strdup(arg[2]);
restart_global = restart_peratom = restart_file = 0;
force_reneighbor = 0;

24
src/fix_ave_chunk.cpp
View File

@ -57,9 +57,7 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) :
nrepeat = utils::inumeric(FLERR,arg[4],false,lmp);
nfreq = utils::inumeric(FLERR,arg[5],false,lmp);
int n = strlen(arg[6]) + 1;
idchunk = new char[n];
strcpy(idchunk,arg[6]);
idchunk = utils::strdup(arg[6]);
global_freq = nfreq;
no_change_box = 1;
@ -190,9 +188,7 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) :
if (iarg+2 > narg)
error->all(FLERR,"Illegal fix ave/chunk command");
biasflag = 1;
int n = strlen(arg[iarg+1]) + 1;
id_bias = new char[n];
strcpy(id_bias,arg[iarg+1]);
id_bias = utils::strdup(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"adof") == 0) {
if (iarg+2 > narg)
@ -220,31 +216,23 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"format") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/chunk command");
delete [] format_user;
int n = strlen(arg[iarg+1]) + 2;
format_user = new char[n];
sprintf(format_user," %s",arg[iarg+1]);
format_user = utils::strdup(arg[iarg+1]);
format = format_user;
iarg += 2;
} else if (strcmp(arg[iarg],"title1") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/chunk command");
delete [] title1;
int n = strlen(arg[iarg+1]) + 1;
title1 = new char[n];
strcpy(title1,arg[iarg+1]);
title1 = utils::strdup(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"title2") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/chunk command");
delete [] title2;
int n = strlen(arg[iarg+1]) + 1;
title2 = new char[n];
strcpy(title2,arg[iarg+1]);
title2 = utils::strdup(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"title3") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/chunk command");
delete [] title3;
int n = strlen(arg[iarg+1]) + 1;
title3 = new char[n];
strcpy(title3,arg[iarg+1]);
title3 = utils::strdup(arg[iarg+1]);
iarg += 2;
} else error->all(FLERR,"Illegal fix ave/chunk command");
}

12
src/fix_ave_correlate.cpp
View File

@ -139,23 +139,17 @@ FixAveCorrelate::FixAveCorrelate(LAMMPS * lmp, int narg, char **arg):
} else if (strcmp(arg[iarg],"title1") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/correlate command");
delete [] title1;
int n = strlen(arg[iarg+1]) + 1;
title1 = new char[n];
strcpy(title1,arg[iarg+1]);
title1 = utils::strdup(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"title2") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/correlate command");
delete [] title2;
int n = strlen(arg[iarg+1]) + 1;
title2 = new char[n];
strcpy(title2,arg[iarg+1]);
title2 = utils::strdup(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"title3") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/correlate command");
delete [] title3;
int n = strlen(arg[iarg+1]) + 1;
title3 = new char[n];
strcpy(title3,arg[iarg+1]);
title3 = utils::strdup(arg[iarg+1]);
iarg += 2;
} else error->all(FLERR,"Illegal fix ave/correlate command");
}

12
src/fix_ave_histo.cpp
View File

@ -993,23 +993,17 @@ void FixAveHisto::options(int iarg, int narg, char **arg)
} else if (strcmp(arg[iarg],"title1") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/histo command");
delete [] title1;
int n = strlen(arg[iarg+1]) + 1;
title1 = new char[n];
strcpy(title1,arg[iarg+1]);
title1 = utils::strdup(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"title2") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/histo command");
delete [] title2;
int n = strlen(arg[iarg+1]) + 1;
title2 = new char[n];
strcpy(title2,arg[iarg+1]);
title2 = utils::strdup(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"title3") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/histo command");
delete [] title3;
int n = strlen(arg[iarg+1]) + 1;
title3 = new char[n];
strcpy(title3,arg[iarg+1]);
title3 = utils::strdup(arg[iarg+1]);
iarg += 2;
} else error->all(FLERR,"Illegal fix ave/histo command");
}

16
src/fix_ave_time.cpp
View File

@ -1067,31 +1067,23 @@ void FixAveTime::options(int iarg, int narg, char **arg)
} else if (strcmp(arg[iarg],"format") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/time command");
delete [] format_user;
int n = strlen(arg[iarg+1]) + 2;
format_user = new char[n];
sprintf(format_user," %s",arg[iarg+1]);
format_user = utils::strdup(arg[iarg+1]);
format = format_user;
iarg += 2;
} else if (strcmp(arg[iarg],"title1") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial command");
delete [] title1;
int n = strlen(arg[iarg+1]) + 1;
title1 = new char[n];
strcpy(title1,arg[iarg+1]);
title1 = utils::strdup(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"title2") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial command");
delete [] title2;
int n = strlen(arg[iarg+1]) + 1;
title2 = new char[n];
strcpy(title2,arg[iarg+1]);
title2 = utils::strdup(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"title3") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial command");
delete [] title3;
int n = strlen(arg[iarg+1]) + 1;
title3 = new char[n];
strcpy(title3,arg[iarg+1]);
title3 = utils::strdup(arg[iarg+1]);
iarg += 2;
} else error->all(FLERR,"Illegal fix ave/time command");
}

8
src/fix_box_relax.cpp
View File

@ -761,9 +761,7 @@ int FixBoxRelax::modify_param(int narg, char **arg)
tflag = 0;
}
delete [] id_temp;
int n = strlen(arg[1]) + 1;
id_temp = new char[n];
strcpy(id_temp,arg[1]);
id_temp = utils::strdup(arg[1]);
int icompute = modify->find_compute(arg[1]);
if (icompute < 0)
@ -792,9 +790,7 @@ int FixBoxRelax::modify_param(int narg, char **arg)
pflag = 0;
}
delete [] id_press;
int n = strlen(arg[1]) + 1;
id_press = new char[n];
strcpy(id_press,arg[1]);
id_press = utils::strdup(arg[1]);
int icompute = modify->find_compute(arg[1]);
if (icompute < 0) error->all(FLERR,"Could not find fix_modify pressure ID");

4
src/fix_controller.cpp
View File

@ -67,9 +67,7 @@ FixController::FixController(LAMMPS *lmp, int narg, char **arg) :
// control variable arg
int n = strlen(arg[iarg]) + 1;
cvID = new char[n];
strcpy(cvID,arg[iarg]);
cvID = utils::strdup(arg[iarg]);
// error check

16
src/fix_deform.cpp
View File

@ -126,12 +126,8 @@ rfix(nullptr), irregular(nullptr), set(nullptr)
error->all(FLERR,"Illegal fix deform command");
delete [] set[index].hstr;
delete [] set[index].hratestr;
int n = strlen(&arg[iarg+2][2]) + 1;
set[index].hstr = new char[n];
strcpy(set[index].hstr,&arg[iarg+2][2]);
n = strlen(&arg[iarg+3][2]) + 1;
set[index].hratestr = new char[n];
strcpy(set[index].hratestr,&arg[iarg+3][2]);
set[index].hstr = utils::strdup(&arg[iarg+2][2]);
set[index].hratestr = utils::strdup(&arg[iarg+3][2]);
iarg += 4;
} else error->all(FLERR,"Illegal fix deform command");
@ -188,12 +184,8 @@ rfix(nullptr), irregular(nullptr), set(nullptr)
error->all(FLERR,"Illegal fix deform command");
delete [] set[index].hstr;
delete [] set[index].hratestr;
int n = strlen(&arg[iarg+2][2]) + 1;
set[index].hstr = new char[n];
strcpy(set[index].hstr,&arg[iarg+2][2]);
n = strlen(&arg[iarg+3][2]) + 1;
set[index].hratestr = new char[n];
strcpy(set[index].hratestr,&arg[iarg+3][2]);
set[index].hstr = utils::strdup(&arg[iarg+2][2]);
set[index].hratestr = utils::strdup(&arg[iarg+3][2]);
iarg += 4;
} else error->all(FLERR,"Illegal fix deform command");

23
src/fix_group.cpp
View File

@ -39,12 +39,9 @@ idregion(nullptr), idvar(nullptr), idprop(nullptr)
// dgroupbit = bitmask of dynamic group
// group ID is last part of fix ID
int n = strlen(id) - strlen("GROUP_") + 1;
char *dgroup = new char[n];
strcpy(dgroup,&id[strlen("GROUP_")]);
gbit = group->bitmask[group->find(dgroup)];
gbitinverse = group->inversemask[group->find(dgroup)];
delete [] dgroup;
auto dgroupid = std::string(id).substr(strlen("GROUP_"));
gbit = group->bitmask[group->find(dgroupid)];
gbitinverse = group->inversemask[group->find(dgroupid)];
// process optional args
@ -61,9 +58,7 @@ idregion(nullptr), idvar(nullptr), idprop(nullptr)
error->all(FLERR,"Region ID for group dynamic does not exist");
regionflag = 1;
delete [] idregion;
int n = strlen(arg[iarg+1]) + 1;
idregion = new char[n];
strcpy(idregion,arg[iarg+1]);
idregion = utils::strdup(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"var") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal group command");
@ -71,9 +66,7 @@ idregion(nullptr), idvar(nullptr), idprop(nullptr)
error->all(FLERR,"Variable name for group dynamic does not exist");
varflag = 1;
delete [] idvar;
int n = strlen(arg[iarg+1]) + 1;
idvar = new char[n];
strcpy(idvar,arg[iarg+1]);
idvar = utils::strdup(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"property") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal group command");
@ -81,9 +74,7 @@ idregion(nullptr), idvar(nullptr), idprop(nullptr)
error->all(FLERR,"Per atom property for group dynamic does not exist");
propflag = 1;
delete [] idprop;
int n = strlen(arg[iarg+1]) + 1;
idprop = new char[n];
strcpy(idprop,arg[iarg+1]);
idprop = utils::strdup(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"every") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal group command");
@ -123,7 +114,7 @@ void FixGroup::init()
if (group->dynamic[igroup])
error->all(FLERR,"Group dynamic parent group cannot be dynamic");
if (strstr(update->integrate_style,"respa"))
if (utils::strmatch(update->integrate_style,"^respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
// set current indices for region and variable

12
src/fix_nh.cpp
View File

@ -275,9 +275,7 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) :
else {
allremap = 0;
delete [] id_dilate;
int n = strlen(arg[iarg+1]) + 1;
id_dilate = new char[n];
strcpy(id_dilate,arg[iarg+1]);
id_dilate = utils::strdup(arg[iarg+1]);
int idilate = group->find(id_dilate);
if (idilate == -1)
error->all(FLERR,"Fix nvt/npt/nph dilate group ID does not exist");
@ -1414,9 +1412,7 @@ int FixNH::modify_param(int narg, char **arg)
tcomputeflag = 0;
}
delete [] id_temp;
int n = strlen(arg[1]) + 1;
id_temp = new char[n];
strcpy(id_temp,arg[1]);
id_temp = utils::strdup(arg[1]);
int icompute = modify->find_compute(arg[1]);
if (icompute < 0)
@ -1448,9 +1444,7 @@ int FixNH::modify_param(int narg, char **arg)
pcomputeflag = 0;
}
delete [] id_press;
int n = strlen(arg[1]) + 1;
id_press = new char[n];
strcpy(id_press,arg[1]);
id_press = utils::strdup(arg[1]);
int icompute = modify->find_compute(arg[1]);
if (icompute < 0) error->all(FLERR,"Could not find fix_modify pressure ID");

8
src/fix_press_berendsen.cpp
View File

@ -467,9 +467,7 @@ int FixPressBerendsen::modify_param(int narg, char **arg)
tflag = 0;
}
delete [] id_temp;
int n = strlen(arg[1]) + 1;
id_temp = new char[n];
strcpy(id_temp,arg[1]);
id_temp = utils::strdup(arg[1]);
int icompute = modify->find_compute(arg[1]);
if (icompute < 0) error->all(FLERR,"Could not find fix_modify temperature ID");
@ -496,9 +494,7 @@ int FixPressBerendsen::modify_param(int narg, char **arg)
pflag = 0;
}
delete [] id_press;
int n = strlen(arg[1]) + 1;
id_press = new char[n];
strcpy(id_press,arg[1]);
id_press = utils::strdup(arg[1]);
int icompute = modify->find_compute(arg[1]);
if (icompute < 0) error->all(FLERR,"Could not find fix_modify pressure ID");

4
src/fix_spring.cpp
View File

@ -70,9 +70,7 @@ FixSpring::FixSpring(LAMMPS *lmp, int narg, char **arg) :
if (narg != 10) error->all(FLERR,"Illegal fix spring command");
styleflag = COUPLE;
int n = strlen(arg[4]) + 1;
group2 = new char[n];
strcpy(group2,arg[4]);
group2 = utils::strdup(arg[4]);
igroup2 = group->find(arg[4]);
if (igroup2 == -1)
error->all(FLERR,"Fix spring couple group ID does not exist");

9
src/fix_spring_chunk.cpp
View File

@ -49,13 +49,8 @@ FixSpringChunk::FixSpringChunk(LAMMPS *lmp, int narg, char **arg) :
k_spring = utils::numeric(FLERR,arg[3],false,lmp);
int n = strlen(arg[4]) + 1;
idchunk = new char[n];
strcpy(idchunk,arg[4]);
n = strlen(arg[5]) + 1;
idcom = new char[n];
strcpy(idcom,arg[5]);
idchunk = utils::strdup(arg[4]);
idcom = utils::strdup(arg[5]);
esprings = 0.0;
nchunk = 0;

4
src/fix_temp_berendsen.cpp
View File

@ -205,9 +205,7 @@ int FixTempBerendsen::modify_param(int narg, char **arg)
tflag = 0;
}
delete [] id_temp;
int n = strlen(arg[1]) + 1;
id_temp = new char[n];
strcpy(id_temp,arg[1]);
id_temp = utils::strdup(arg[1]);
int icompute = modify->find_compute(id_temp);
if (icompute < 0)

4
src/fix_temp_csld.cpp
View File

@ -261,9 +261,7 @@ int FixTempCSLD::modify_param(int narg, char **arg)
tflag = 0;
}
delete [] id_temp;
int n = strlen(arg[1]) + 1;
id_temp = new char[n];
strcpy(id_temp,arg[1]);
id_temp = utils::strdup(arg[1]);
int icompute = modify->find_compute(id_temp);
if (icompute < 0)

4
src/fix_temp_csvr.cpp
View File

@ -216,9 +216,7 @@ int FixTempCSVR::modify_param(int narg, char **arg)
tflag = 0;
}
delete [] id_temp;
int n = strlen(arg[1]) + 1;
id_temp = new char[n];
strcpy(id_temp,arg[1]);
id_temp = utils::strdup(arg[1]);
int icompute = modify->find_compute(id_temp);
if (icompute < 0)

4
src/fix_temp_rescale.cpp
View File

@ -202,9 +202,7 @@ int FixTempRescale::modify_param(int narg, char **arg)
tflag = 0;
}
delete [] id_temp;
int n = strlen(arg[1]) + 1;
id_temp = new char[n];
strcpy(id_temp,arg[1]);
id_temp = utils::strdup(arg[1]);
int icompute = modify->find_compute(id_temp);
if (icompute < 0)

4
src/fix_wall_region.cpp
View File

@ -54,9 +54,7 @@ FixWallRegion::FixWallRegion(LAMMPS *lmp, int narg, char **arg) :
iregion = domain->find_region(arg[3]);
if (iregion == -1)
error->all(FLERR,"Region ID for fix wall/region does not exist");
int n = strlen(arg[3]) + 1;
idregion = new char[n];
strcpy(idregion,arg[3]);
idregion = utils::strdup(arg[3]);
if (strcmp(arg[4],"lj93") == 0) style = LJ93;
else if (strcmp(arg[4],"lj126") == 0) style = LJ126;

20
src/force.cpp
View File

@ -61,20 +61,12 @@ Force::Force(LAMMPS *lmp) : Pointers(lmp)
improper = nullptr;
kspace = nullptr;
char *str = (char *) "none";
int n = strlen(str) + 1;
pair_style = new char[n];
strcpy(pair_style,str);
bond_style = new char[n];
strcpy(bond_style,str);
angle_style = new char[n];
strcpy(angle_style,str);
dihedral_style = new char[n];
strcpy(dihedral_style,str);
improper_style = new char[n];
strcpy(improper_style,str);
kspace_style = new char[n];
strcpy(kspace_style,str);
pair_style = utils::strdup("none");
bond_style = utils::strdup("none");
angle_style = utils::strdup("none");
dihedral_style = utils::strdup("none");
improper_style = utils::strdup("none");
kspace_style = utils::strdup("none");
pair_restart = nullptr;
create_factories();

5
src/imbalance_store.cpp
View File

@ -36,10 +36,7 @@ ImbalanceStore::~ImbalanceStore()
int ImbalanceStore::options(int narg, char **arg)
{
if (narg < 1) error->all(FLERR,"Illegal balance weight command");
int len = strlen(arg[0]) + 1;
name = new char[len];
memcpy(name,arg[0],len);
name = utils::strdup(arg[0]);
return 1;
}

5
src/imbalance_var.cpp
View File

@ -40,10 +40,7 @@ ImbalanceVar::~ImbalanceVar()
int ImbalanceVar::options(int narg, char **arg)
{
if (narg < 1) error->all(FLERR,"Illegal balance weight command");
int len = strlen(arg[0]) + 1;
name = new char[len];
memcpy(name,arg[0],len);
name = utils::strdup(arg[0]);
init(0);
return 1;

16
src/input.cpp
View File

@ -1013,9 +1013,7 @@ void Input::jump()
if (narg == 2) {
label_active = 1;
if (labelstr) delete [] labelstr;
int n = strlen(arg[1]) + 1;
labelstr = new char[n];
strcpy(labelstr,arg[1]);
labelstr = utils::strdup(arg[1]);
}
}
@ -1840,17 +1838,11 @@ void Input::suffix()
if (strcmp(arg[0],"hybrid") == 0) {
if (narg != 3) error->all(FLERR,"Illegal suffix command");
int n = strlen(arg[1]) + 1;
lmp->suffix = new char[n];
strcpy(lmp->suffix,arg[1]);
n = strlen(arg[2]) + 1;
lmp->suffix2 = new char[n];
strcpy(lmp->suffix2,arg[2]);
lmp->suffix = utils::strdup(arg[1]);
lmp->suffix2 = utils::strdup(arg[2]);
} else {
if (narg != 1) error->all(FLERR,"Illegal suffix command");
int n = strlen(arg[0]) + 1;
lmp->suffix = new char[n];
strcpy(lmp->suffix,arg[0]);
lmp->suffix = utils::strdup(arg[0]);
}
}
}

3
src/library.cpp
View File

@ -444,12 +444,11 @@ is passed to :cpp:func:`lammps_commands_string` for processing.
void lammps_commands_list(void *handle, int ncmd, const char **cmds)
{
LAMMPS *lmp = (LAMMPS *) handle;
std::string allcmds;
for (int i = 0; i < ncmd; i++) {
allcmds.append(cmds[i]);
if (allcmds.back() != '\n') allcmds.append(1,'\n');
if (allcmds.empty() || (allcmds.back() != '\n')) allcmds.append(1,'\n');
}
lammps_commands_string(handle,allcmds.c_str());

3
src/neighbor.cpp
View File

@ -1479,7 +1479,8 @@ void Neighbor::print_pairwise_info()
rq = requests[i];
if (rq->pair) {
char *pname = force->pair_match_ptr((Pair *) rq->requestor);
out += fmt::format(" ({}) pair {}",i+1,pname);
if (pname) out += fmt::format(" ({}) pair {}",i+1,pname);
else out += fmt::format(" ({}) pair (none)",i+1);
} else if (rq->fix) {
out += fmt::format(" ({}) fix {}",i+1,((Fix *) rq->requestor)->style);
} else if (rq->compute) {

24
src/read_data.cpp
View File

@ -337,6 +337,12 @@ void ReadData::command(int narg, char **arg)
Dihedral *saved_dihedral = nullptr;
Improper *saved_improper = nullptr;
KSpace *saved_kspace = nullptr;
char *saved_pair_style = nullptr;
char *saved_bond_style = nullptr;
char *saved_angle_style = nullptr;
char *saved_dihedral_style = nullptr;
char *saved_improper_style = nullptr;
char *saved_kspace_style = nullptr;
if (coeffflag == 0) {
char *coeffs[2];
@ -344,33 +350,45 @@ void ReadData::command(int narg, char **arg)
coeffs[1] = (char *) "nocoeff";
saved_pair = force->pair;
saved_pair_style = force->pair_style;
force->pair = nullptr;
force->pair_style = nullptr;
force->create_pair("zero",0);
if (force->pair) force->pair->settings(2,coeffs);
coeffs[0] = coeffs[1];
saved_bond = force->bond;
saved_bond_style = force->bond_style;
force->bond = nullptr;
force->bond_style = nullptr;
force->create_bond("zero",0);
if (force->bond) force->bond->settings(1,coeffs);
saved_angle = force->angle;
saved_angle_style = force->angle_style;
force->angle = nullptr;
force->angle_style = nullptr;
force->create_angle("zero",0);
if (force->angle) force->angle->settings(1,coeffs);
saved_dihedral = force->dihedral;
saved_dihedral_style = force->dihedral_style;
force->dihedral = nullptr;
force->dihedral_style = nullptr;
force->create_dihedral("zero",0);
if (force->dihedral) force->dihedral->settings(1,coeffs);
saved_improper = force->improper;
saved_improper_style = force->improper_style;
force->improper = nullptr;
force->improper_style = nullptr;
force->create_improper("zero",0);
if (force->improper) force->improper->settings(1,coeffs);
saved_kspace = force->kspace;
saved_kspace_style = force->kspace_style;
force->kspace = nullptr;
force->kspace_style = nullptr;
}
// -----------------------------------------------------------------
@ -873,20 +891,26 @@ void ReadData::command(int narg, char **arg)
if (coeffflag == 0) {
if (force->pair) delete force->pair;
force->pair = saved_pair;
force->pair_style = saved_pair_style;
if (force->bond) delete force->bond;
force->bond = saved_bond;
force->bond_style = saved_bond_style;
if (force->angle) delete force->angle;
force->angle = saved_angle;
force->angle_style = saved_angle_style;
if (force->dihedral) delete force->dihedral;
force->dihedral = saved_dihedral;
force->dihedral_style = saved_dihedral_style;
if (force->improper) delete force->improper;
force->improper = saved_improper;
force->improper_style = saved_improper_style;
force->kspace = saved_kspace;
force->kspace_style = saved_kspace_style;
}
// total time

5
src/tokenizer.cpp
View File

@ -201,7 +201,6 @@ std::string ValueTokenizer::next_string() {
std::string value = tokens.next();
return value;
} throw TokenizerException("Not enough tokens","");
return "";
}
/*! Retrieve next token and convert to int
@ -217,7 +216,6 @@ int ValueTokenizer::next_int() {
int value = atoi(current.c_str());
return value;
} throw TokenizerException("Not enough tokens","");
return 0;
}
/*! Retrieve next token and convert to bigint
@ -233,7 +231,6 @@ bigint ValueTokenizer::next_bigint() {
bigint value = ATOBIGINT(current.c_str());
return value;
} throw TokenizerException("Not enough tokens","");
return 0;
}
/*! Retrieve next token and convert to tagint
@ -249,7 +246,6 @@ tagint ValueTokenizer::next_tagint() {
tagint value = ATOTAGINT(current.c_str());
return value;
} throw TokenizerException("Not enough tokens","");
return 0;
}
/*! Retrieve next token and convert to double
@ -265,7 +261,6 @@ double ValueTokenizer::next_double() {
double value = atof(current.c_str());
return value;
} throw TokenizerException("Not enough tokens","");
return 0.0;
}
/*! Skip over a given number of tokens

1
src/utils.cpp
View File

@ -473,6 +473,7 @@ int utils::expand_args(const char *file, int line, int narg, char **arg,
for (iarg = 0; iarg < narg; iarg++) {
std::string word(arg[iarg]);
expandflag = 0;
// only match compute/fix reference with a '*' wildcard
// number range in the first pair of square brackets

4
unittest/commands/test_reset_ids.cpp
View File

@ -482,8 +482,6 @@ TEST_F(ResetIDsTest, TopologyData)
auto num_bond = lmp->atom->num_bond;
auto num_angle = lmp->atom->num_angle;
auto num_dihedral = lmp->atom->num_dihedral;
auto num_improper = lmp->atom->num_improper;
auto bond_atom = lmp->atom->bond_atom;
auto angle_atom1 = lmp->atom->angle_atom1;
auto angle_atom2 = lmp->atom->angle_atom2;
@ -568,8 +566,6 @@ TEST_F(ResetIDsTest, TopologyData)
num_bond = lmp->atom->num_bond;
num_angle = lmp->atom->num_angle;
num_dihedral = lmp->atom->num_dihedral;
num_improper = lmp->atom->num_improper;
bond_atom = lmp->atom->bond_atom;
angle_atom1 = lmp->atom->angle_atom1;
angle_atom2 = lmp->atom->angle_atom2;

2
unittest/force-styles/test_angle_style.cpp
View File

@ -308,7 +308,6 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
// init_forces
block.clear();
auto f = lmp->atom->f;
auto tag = lmp->atom->tag;
for (int i = 1; i <= natoms; ++i) {
const int j = lmp->atom->map(i);
block += fmt::format("{:3} {:23.16e} {:23.16e} {:23.16e}\n", i, f[j][0], f[j][1], f[j][2]);
@ -329,7 +328,6 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
block.clear();
f = lmp->atom->f;
tag = lmp->atom->tag;
for (int i = 1; i <= natoms; ++i) {
const int j = lmp->atom->map(i);
block += fmt::format("{:3} {:23.16e} {:23.16e} {:23.16e}\n", i, f[j][0], f[j][1], f[j][2]);

2
unittest/force-styles/test_bond_style.cpp
View File

@ -308,7 +308,6 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
// init_forces
block.clear();
auto f = lmp->atom->f;
auto tag = lmp->atom->tag;
for (int i = 1; i <= natoms; ++i) {
const int j = lmp->atom->map(i);
block += fmt::format("{:3} {:23.16e} {:23.16e} {:23.16e}\n", i, f[j][0], f[j][1], f[j][2]);
@ -329,7 +328,6 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
block.clear();
f = lmp->atom->f;
tag = lmp->atom->tag;
for (int i = 1; i <= natoms; ++i) {
const int j = lmp->atom->map(i);
block += fmt::format("{:3} {:23.16e} {:23.16e} {:23.16e}\n", i, f[j][0], f[j][1], f[j][2]);

2
unittest/force-styles/test_dihedral_style.cpp
View File

@ -311,7 +311,6 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
// init_forces
block.clear();
auto f = lmp->atom->f;
auto tag = lmp->atom->tag;
for (int i = 1; i <= natoms; ++i) {
const int j = lmp->atom->map(i);
block += fmt::format("{:3} {:23.16e} {:23.16e} {:23.16e}\n", i, f[j][0], f[j][1], f[j][2]);
@ -332,7 +331,6 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
block.clear();
f = lmp->atom->f;
tag = lmp->atom->tag;
for (int i = 1; i <= natoms; ++i) {
const int j = lmp->atom->map(i);
block += fmt::format("{:3} {:23.16e} {:23.16e} {:23.16e}\n", i, f[j][0], f[j][1], f[j][2]);

2
unittest/force-styles/test_improper_style.cpp
View File

@ -302,7 +302,6 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
// init_forces
block.clear();
auto f = lmp->atom->f;
auto tag = lmp->atom->tag;
for (int i = 1; i <= natoms; ++i) {
const int j = lmp->atom->map(i);
block += fmt::format("{:3} {:23.16e} {:23.16e} {:23.16e}\n", i, f[j][0], f[j][1], f[j][2]);
@ -323,7 +322,6 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
block.clear();
f = lmp->atom->f;
tag = lmp->atom->tag;
for (int i = 1; i <= natoms; ++i) {
const int j = lmp->atom->map(i);
block += fmt::format("{:3} {:23.16e} {:23.16e} {:23.16e}\n", i, f[j][0], f[j][1], f[j][2]);

2
unittest/force-styles/test_pair_style.cpp
View File

@ -308,7 +308,6 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
// init_forces
block.clear();
auto f = lmp->atom->f;
auto tag = lmp->atom->tag;
for (int i = 1; i <= natoms; ++i) {
const int j = lmp->atom->map(i);
block += fmt::format("{:3} {:23.16e} {:23.16e} {:23.16e}\n", i, f[j][0], f[j][1], f[j][2]);
@ -332,7 +331,6 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
block.clear();
f = lmp->atom->f;
tag = lmp->atom->tag;
for (int i = 1; i <= natoms; ++i) {
const int j = lmp->atom->map(i);
block += fmt::format("{:3} {:23.16e} {:23.16e} {:23.16e}\n", i, f[j][0], f[j][1], f[j][2]);