Added cautionary comments

This commit is contained in:
jtclemm
2020-08-08 09:15:56 -06:00
parent 6b1191b1c0
commit 41904f7946
20 changed files with 47 additions and 9 deletions

4
src/GRANULAR/fix_wall_gran.cpp Normal file → Executable file
View File

@ -1541,6 +1541,7 @@ int FixWallGran::pack_restart(int i, double *buf)
if (!use_history) return 0; if (!use_history) return 0;
int n = 0; int n = 0;
// pack buf[0] this way b/c other fixes unpack it
buf[n++] = size_history + 1; buf[n++] = size_history + 1;
for (int m = 0; m < size_history; m++) for (int m = 0; m < size_history; m++)
buf[n++] = history_one[i][m]; buf[n++] = history_one[i][m];
@ -1558,7 +1559,8 @@ void FixWallGran::unpack_restart(int nlocal, int nth)
double **extra = atom->extra; double **extra = atom->extra;
// skip to Nth set of extra values // skip to Nth set of extra values
// unpack the Nth first values this way b/c other fixes pack them
int m = 0; int m = 0;
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]); for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);
m++; m++;

4
src/GRANULAR/fix_wall_gran_region.cpp Normal file → Executable file
View File

@ -479,6 +479,7 @@ int FixWallGranRegion::pack_restart(int i, double *buf)
for (m = 0; m < size_history; m++) for (m = 0; m < size_history; m++)
buf[n++] = history_many[i][iwall][m]; buf[n++] = history_many[i][iwall][m];
} }
// pack buf[0] this way b/c other fixes unpack it
buf[0] = n; buf[0] = n;
return n; return n;
} }
@ -496,7 +497,8 @@ void FixWallGranRegion::unpack_restart(int nlocal, int nth)
double **extra = atom->extra; double **extra = atom->extra;
// skip to Nth set of extra values // skip to Nth set of extra values
// unpack the Nth first values this way b/c other fixes pack them
int m = 0; int m = 0;
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]); for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);
m++; m++;

4
src/MISC/fix_gld.cpp Normal file → Executable file
View File

@ -547,6 +547,7 @@ int FixGLD::unpack_exchange(int nlocal, double *buf)
int FixGLD::pack_restart(int i, double *buf) int FixGLD::pack_restart(int i, double *buf)
{ {
int m = 0; int m = 0;
// pack buf[0] this way b/c other fixes unpack it
buf[m++] = 3*prony_terms + 1; buf[m++] = 3*prony_terms + 1;
for (int k = 0; k < 3*prony_terms; k=k+3) for (int k = 0; k < 3*prony_terms; k=k+3)
{ {
@ -566,7 +567,8 @@ void FixGLD::unpack_restart(int nlocal, int nth)
double **extra = atom->extra; double **extra = atom->extra;
// skip to the nth set of extended variables // skip to the nth set of extended variables
// unpack the Nth first values this way b/c other fixes pack them
int m = 0; int m = 0;
for (int i = 0; i< nth; i++) m += static_cast<int> (extra[nlocal][m]); for (int i = 0; i< nth; i++) m += static_cast<int> (extra[nlocal][m]);
m++; m++;

4
src/MISC/fix_ttm.cpp Normal file → Executable file
View File

@ -656,6 +656,7 @@ void FixTTM::restart(char *buf)
int FixTTM::pack_restart(int i, double *buf) int FixTTM::pack_restart(int i, double *buf)
{ {
// pack buf[0] this way b/c other fixes unpack it
buf[0] = 4; buf[0] = 4;
buf[1] = flangevin[i][0]; buf[1] = flangevin[i][0];
buf[2] = flangevin[i][1]; buf[2] = flangevin[i][1];
@ -672,7 +673,8 @@ void FixTTM::unpack_restart(int nlocal, int nth)
double **extra = atom->extra; double **extra = atom->extra;
// skip to Nth set of extra values // skip to Nth set of extra values
// unpack the Nth first values this way b/c other fixes pack them
int m = 0; int m = 0;
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]); for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);
m++; m++;

4
src/MOLECULE/fix_cmap.cpp Normal file → Executable file
View File

@ -1291,6 +1291,7 @@ int FixCMAP::pack_restart(int i, double *buf)
buf[n++] = ubuf(crossterm_atom4[i][m]).d; buf[n++] = ubuf(crossterm_atom4[i][m]).d;
buf[n++] = ubuf(crossterm_atom5[i][m]).d; buf[n++] = ubuf(crossterm_atom5[i][m]).d;
} }
// pack buf[0] this way b/c other fixes unpack it
buf[0] = n; buf[0] = n;
return n; return n;
@ -1305,7 +1306,8 @@ void FixCMAP::unpack_restart(int nlocal, int nth)
double **extra = atom->extra; double **extra = atom->extra;
// skip to Nth set of extra values // skip to Nth set of extra values
// unpack the Nth first values this way b/c other fixes pack them
int n = 0; int n = 0;
for (int i = 0; i < nth; i++) n += static_cast<int> (extra[nlocal][n]); for (int i = 0; i < nth; i++) n += static_cast<int> (extra[nlocal][n]);

View File

@ -579,6 +579,7 @@ void FixPeriNeigh::restart(char *buf)
int FixPeriNeigh::pack_restart(int i, double *buf) int FixPeriNeigh::pack_restart(int i, double *buf)
{ {
int m = 0; int m = 0;
// pack buf[0] this way b/c other fixes unpack it
if (isVES) buf[m++] = 4*npartner[i] + 4; if (isVES) buf[m++] = 4*npartner[i] + 4;
else if (isEPS) buf[m++] = 3*npartner[i] + 5; else if (isEPS) buf[m++] = 3*npartner[i] + 5;
else buf[m++] = 2*npartner[i] + 4; else buf[m++] = 2*npartner[i] + 4;
@ -608,6 +609,7 @@ void FixPeriNeigh::unpack_restart(int nlocal, int nth)
double **extra = atom->extra; double **extra = atom->extra;
// skip to Nth set of extra values // skip to Nth set of extra values
// unpack the Nth first values this way b/c other fixes pack them
int m = 0; int m = 0;
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]); for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);

0
src/USER-ATC/fix_atc.cpp Normal file → Executable file
View File

4
src/USER-MISC/fix_gle.cpp Normal file → Executable file
View File

@ -822,6 +822,7 @@ int FixGLE::unpack_exchange(int nlocal, double *buf)
int FixGLE::pack_restart(int i, double *buf) int FixGLE::pack_restart(int i, double *buf)
{ {
int m = 0; int m = 0;
// pack buf[0] this way b/c other fixes unpack it
buf[m++] = 3*ns + 1; buf[m++] = 3*ns + 1;
for (int k = 0; k < 3*ns; k=k+3) for (int k = 0; k < 3*ns; k=k+3)
{ {
@ -841,7 +842,8 @@ void FixGLE::unpack_restart(int nlocal, int nth)
double **extra = atom->extra; double **extra = atom->extra;
// skip to the nth set of extended variables // skip to the nth set of extended variables
// unpack the Nth first values this way b/c other fixes pack them
int m = 0; int m = 0;
for (int i = 0; i< nth; i++) m += static_cast<int> (extra[nlocal][m]); for (int i = 0; i< nth; i++) m += static_cast<int> (extra[nlocal][m]);
m++; m++;

2
src/USER-MISC/fix_pimd.cpp Normal file → Executable file
View File

@ -794,6 +794,7 @@ int FixPIMD::pack_restart(int i, double *buf)
{ {
int offset=0; int offset=0;
int pos = i * 3; int pos = i * 3;
// pack buf[0] this way b/c other fixes unpack it
buf[offset++] = size_peratom_cols+1; buf[offset++] = size_peratom_cols+1;
memcpy(buf+offset, nhc_eta[pos], nhc_size_one_1); offset += nhc_offset_one_1; memcpy(buf+offset, nhc_eta[pos], nhc_size_one_1); offset += nhc_offset_one_1;
@ -811,6 +812,7 @@ void FixPIMD::unpack_restart(int nlocal, int nth)
double **extra = atom->extra; double **extra = atom->extra;
// skip to Nth set of extra values // skip to Nth set of extra values
// unpack the Nth first values this way b/c other fixes pack them
int m = 0; int m = 0;
for (int i=0; i<nth; i++) m += static_cast<int> (extra[nlocal][m]); for (int i=0; i<nth; i++) m += static_cast<int> (extra[nlocal][m]);

7
src/USER-MISC/fix_srp.cpp Normal file → Executable file
View File

@ -555,6 +555,7 @@ void FixSRP::post_run()
int FixSRP::pack_restart(int i, double *buf) int FixSRP::pack_restart(int i, double *buf)
{ {
int m = 0; int m = 0;
// pack buf[0] this way b/c other fixes unpack it
buf[m++] = 3; buf[m++] = 3;
buf[m++] = array[i][0]; buf[m++] = array[i][0];
buf[m++] = array[i][1]; buf[m++] = array[i][1];
@ -569,10 +570,12 @@ void FixSRP::unpack_restart(int nlocal, int nth)
{ {
double **extra = atom->extra; double **extra = atom->extra;
// skip to Nth set of extra values // skip to Nth set of extra values
// unpack the Nth first values this way b/c other fixes pack them
int m = 0; int m = 0;
for (int i = 0; i < nth; i++){ for (int i = 0; i < nth; i++){
m += extra[nlocal][m]; m += static_cast<int> (extra[nlocal][m]);
} }
m++; m++;

3
src/USER-MISC/fix_ti_spring.cpp Normal file → Executable file
View File

@ -315,7 +315,7 @@ int FixTISpring::unpack_exchange(int nlocal, double *buf)
int FixTISpring::pack_restart(int i, double *buf) int FixTISpring::pack_restart(int i, double *buf)
{ {
buf[0] = 4; // pack buf[0] this way b/c other fixes unpack it
buf[1] = xoriginal[i][0]; buf[1] = xoriginal[i][0];
buf[2] = xoriginal[i][1]; buf[2] = xoriginal[i][1];
buf[3] = xoriginal[i][2]; buf[3] = xoriginal[i][2];
@ -331,6 +331,7 @@ void FixTISpring::unpack_restart(int nlocal, int nth)
double **extra = atom->extra; double **extra = atom->extra;
// skip to Nth set of extra values // skip to Nth set of extra values
// unpack the Nth first values this way b/c other fixes pack them
int m = 0; int m = 0;
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]); for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);

2
src/USER-MISC/fix_ttm_mod.cpp Normal file → Executable file
View File

@ -980,6 +980,7 @@ void FixTTMMod::restart(char *buf)
int FixTTMMod::pack_restart(int i, double *buf) int FixTTMMod::pack_restart(int i, double *buf)
{ {
// pack buf[0] this way b/c other fixes unpack it
buf[0] = 4; buf[0] = 4;
buf[1] = flangevin[i][0]; buf[1] = flangevin[i][0];
buf[2] = flangevin[i][1]; buf[2] = flangevin[i][1];
@ -996,6 +997,7 @@ void FixTTMMod::unpack_restart(int nlocal, int nth)
double **extra = atom->extra; double **extra = atom->extra;
// skip to Nth set of extra values // skip to Nth set of extra values
// unpack the Nth first values this way b/c other fixes pack them
int m = 0; int m = 0;
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]); for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);

2
src/USER-SDPD/fix_meso_move.cpp Normal file → Executable file
View File

@ -948,6 +948,7 @@ int FixMesoMove::unpack_exchange (int nlocal, double *buf) {
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
int FixMesoMove::pack_restart (int i, double *buf) { int FixMesoMove::pack_restart (int i, double *buf) {
// pack buf[0] this way b/c other fixes unpack it
buf[0] = 4; buf[0] = 4;
buf[1] = xoriginal[i][0]; buf[1] = xoriginal[i][0];
buf[2] = xoriginal[i][1]; buf[2] = xoriginal[i][1];
@ -963,6 +964,7 @@ void FixMesoMove::unpack_restart (int nlocal, int nth) {
double **extra = atom->extra; double **extra = atom->extra;
// skip to Nth set of extra values // skip to Nth set of extra values
// unpack the Nth first values this way b/c other fixes pack them
int m = 0; int m = 0;
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]); for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);

2
src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp Normal file → Executable file
View File

@ -450,6 +450,7 @@ int FixSMD_TLSPH_ReferenceConfiguration::unpack_exchange(int nlocal, double *buf
int FixSMD_TLSPH_ReferenceConfiguration::pack_restart(int i, double *buf) { int FixSMD_TLSPH_ReferenceConfiguration::pack_restart(int i, double *buf) {
int m = 0; int m = 0;
// pack buf[0] this way b/c other fixes unpack it
buf[m++] = 4 * npartner[i] + 2; buf[m++] = 4 * npartner[i] + 2;
buf[m++] = npartner[i]; buf[m++] = npartner[i];
for (int n = 0; n < npartner[i]; n++) { for (int n = 0; n < npartner[i]; n++) {
@ -470,6 +471,7 @@ void FixSMD_TLSPH_ReferenceConfiguration::unpack_restart(int /*nlocal*/, int /*n
// ipage = NULL if being called from granular pair style init() // ipage = NULL if being called from granular pair style init()
// skip to Nth set of extra values // skip to Nth set of extra values
// unpack the Nth first values this way b/c other fixes pack them
// double **extra = atom->extra; // double **extra = atom->extra;
// //

2
src/fix_move.cpp Normal file → Executable file
View File

@ -1193,6 +1193,7 @@ int FixMove::pack_restart(int i, double *buf)
buf[n++] = qoriginal[i][2]; buf[n++] = qoriginal[i][2];
buf[n++] = qoriginal[i][3]; buf[n++] = qoriginal[i][3];
} }
// pack buf[0] this way b/c other fixes unpack it
buf[0] = n; buf[0] = n;
return n; return n;
} }
@ -1206,6 +1207,7 @@ void FixMove::unpack_restart(int nlocal, int nth)
double **extra = atom->extra; double **extra = atom->extra;
// skip to Nth set of extra values // skip to Nth set of extra values
// unpack the Nth first values this way b/c other fixes pack them
int m = 0; int m = 0;
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]); for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);

2
src/fix_neigh_history.cpp Normal file → Executable file
View File

@ -853,6 +853,7 @@ int FixNeighHistory::pack_restart(int i, double *buf)
memcpy(&buf[m],&valuepartner[i][dnum*n],dnumbytes); memcpy(&buf[m],&valuepartner[i][dnum*n],dnumbytes);
m += dnum; m += dnum;
} }
// pack buf[0] this way b/c other fixes unpack it
buf[0] = m; buf[0] = m;
return m; return m;
} }
@ -868,6 +869,7 @@ void FixNeighHistory::unpack_restart(int nlocal, int nth)
if (ipage_atom == NULL) allocate_pages(); if (ipage_atom == NULL) allocate_pages();
// skip to Nth set of extra values // skip to Nth set of extra values
// unpack the Nth first values this way b/c other fixes pack them
double **extra = atom->extra; double **extra = atom->extra;

2
src/fix_property_atom.cpp Normal file → Executable file
View File

@ -579,6 +579,7 @@ int FixPropertyAtom::unpack_exchange(int nlocal, double *buf)
int FixPropertyAtom::pack_restart(int i, double *buf) int FixPropertyAtom::pack_restart(int i, double *buf)
{ {
// pack buf[0] this way b/c other fixes unpack it
buf[0] = nvalue+1; buf[0] = nvalue+1;
int m = 1; int m = 1;
@ -602,6 +603,7 @@ void FixPropertyAtom::unpack_restart(int nlocal, int nth)
double **extra = atom->extra; double **extra = atom->extra;
// skip to Nth set of extra values // skip to Nth set of extra values
// unpack the Nth first values this way b/c other fixes pack them
int m = 0; int m = 0;
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]); for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);

2
src/fix_spring_self.cpp Normal file → Executable file
View File

@ -264,6 +264,7 @@ int FixSpringSelf::unpack_exchange(int nlocal, double *buf)
int FixSpringSelf::pack_restart(int i, double *buf) int FixSpringSelf::pack_restart(int i, double *buf)
{ {
// pack buf[0] this way b/c other fixes unpack it
buf[0] = 4; buf[0] = 4;
buf[1] = xoriginal[i][0]; buf[1] = xoriginal[i][0];
buf[2] = xoriginal[i][1]; buf[2] = xoriginal[i][1];
@ -280,6 +281,7 @@ void FixSpringSelf::unpack_restart(int nlocal, int nth)
double **extra = atom->extra; double **extra = atom->extra;
// skip to Nth set of extra values // skip to Nth set of extra values
// unpack the Nth first values this way b/c other fixes pack them
int m = 0; int m = 0;
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]); for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);

2
src/fix_store.cpp Normal file → Executable file
View File

@ -280,6 +280,7 @@ int FixStore::pack_restart(int i, double *buf)
return 1; return 1;
} }
// pack buf[0] this way b/c other fixes unpack it
buf[0] = nvalues+1; buf[0] = nvalues+1;
if (vecflag) buf[1] = vstore[i]; if (vecflag) buf[1] = vstore[i];
else else
@ -299,6 +300,7 @@ void FixStore::unpack_restart(int nlocal, int nth)
double **extra = atom->extra; double **extra = atom->extra;
// skip to Nth set of extra values // skip to Nth set of extra values
// unpack the Nth first values this way b/c other fixes pack them
int m = 0; int m = 0;
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]); for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);

2
src/fix_store_state.cpp Normal file → Executable file
View File

@ -611,6 +611,7 @@ int FixStoreState::unpack_exchange(int nlocal, double *buf)
int FixStoreState::pack_restart(int i, double *buf) int FixStoreState::pack_restart(int i, double *buf)
{ {
// pack buf[0] this way b/c other fixes unpack it
buf[0] = nvalues+1; buf[0] = nvalues+1;
for (int m = 0; m < nvalues; m++) buf[m+1] = values[i][m]; for (int m = 0; m < nvalues; m++) buf[m+1] = values[i][m];
return nvalues+1; return nvalues+1;
@ -625,6 +626,7 @@ void FixStoreState::unpack_restart(int nlocal, int nth)
double **extra = atom->extra; double **extra = atom->extra;
// skip to Nth set of extra values // skip to Nth set of extra values
// unpack the Nth first values this way b/c other fixes pack them
int m = 0; int m = 0;
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]); for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);