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Merge branch 'develop' of https://github.com/lammps/lammps into lammps-develop

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This commit is contained in:
Jacob Gissinger
2021-11-04 21:20:29 -04:00
parent 67ae6eb7b6 a4ceda9706
commit 8d4956046b
727 changed files with 31087 additions and 8662 deletions
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31
src/write_data.cpp
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@ -220,9 +220,9 @@ void WriteData::write(const std::string &file)
// extra sections managed by fixes
if (fixflag)
for (int i = 0; i < modify->nfix; i++)
if (modify->fix[i]->wd_section)
for (int m = 0; m < modify->fix[i]->wd_section; m++) fix(i,m);
for (auto &ifix : modify->get_fix_list())
if (ifix->wd_section)
for (int m = 0; m < ifix->wd_section; m++) fix(ifix,m);
// close data file
@ -274,22 +274,19 @@ void WriteData::header()
// fix info
if (fixflag)
for (int i = 0; i < modify->nfix; i++)
if (modify->fix[i]->wd_header)
for (int m = 0; m < modify->fix[i]->wd_header; m++)
modify->fix[i]->write_data_header(fp,m);
for (auto &ifix : modify->get_fix_list())
if (ifix->wd_header)
for (int m = 0; m < ifix->wd_header; m++)
ifix->write_data_header(fp,m);
// box info
auto box = fmt::format("\n{} {} xlo xhi"
"\n{} {} ylo yhi"
"\n{} {} zlo zhi\n",
auto box = fmt::format("\n{} {} xlo xhi\n{} {} ylo yhi\n{} {} zlo zhi\n",
domain->boxlo[0],domain->boxhi[0],
domain->boxlo[1],domain->boxhi[1],
domain->boxlo[2],domain->boxhi[2]);
if (domain->triclinic)
box += fmt::format("{} {} {} xy xz yz\n",
domain->xy,domain->xz,domain->yz);
box += fmt::format("{} {} {} xy xz yz\n",domain->xy,domain->xz,domain->yz);
fputs(box.c_str(),fp);
}
@ -729,13 +726,13 @@ void WriteData::bonus(int flag)
write out Mth section of data file owned by Fix ifix
------------------------------------------------------------------------- */
void WriteData::fix(int ifix, int mth)
void WriteData::fix(Fix *ifix, int mth)
{
// communication buffer for Fix info
// maxrow X ncol = largest buffer needed by any proc
int sendrow,ncol;
modify->fix[ifix]->write_data_section_size(mth,sendrow,ncol);
ifix->write_data_section_size(mth,sendrow,ncol);
int maxrow;
MPI_Allreduce(&sendrow,&maxrow,1,MPI_INT,MPI_MAX,world);
@ -745,7 +742,7 @@ void WriteData::fix(int ifix, int mth)
// pack my fix data into buf
modify->fix[ifix]->write_data_section_pack(mth,buf);
ifix->write_data_section_pack(mth,buf);
// write one chunk of info per proc to file
// proc 0 pings each proc, receives its chunk, writes to file
@ -758,7 +755,7 @@ void WriteData::fix(int ifix, int mth)
MPI_Status status;
MPI_Request request;
modify->fix[ifix]->write_data_section_keyword(mth,fp);
ifix->write_data_section_keyword(mth,fp);
for (int iproc = 0; iproc < nprocs; iproc++) {
if (iproc) {
MPI_Irecv(&buf[0][0],maxrow*ncol,MPI_DOUBLE,iproc,0,world,&request);
@ -768,7 +765,7 @@ void WriteData::fix(int ifix, int mth)
recvrow /= ncol;
} else recvrow = sendrow;
modify->fix[ifix]->write_data_section(mth,fp,recvrow,buf,index);
ifix->write_data_section(mth,fp,recvrow,buf,index);
index += recvrow;
}