tx258/lammps-gran-kokkos
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

replace strtok based file reader with ValueTokernizer

Browse Source
This commit is contained in:
Axel Kohlmeyer
2022-03-20 16:34:41 -04:00
parent adf4a23f58
commit 89c7d8f707
1 changed files with 54 additions and 58 deletions
Download Patch File Download Diff File Expand all files Collapse all files

112
src/RIGID/fix_rigid.cpp
View File

@ -32,6 +32,7 @@
#include "random_mars.h"
#include "respa.h"
#include "rigid_const.h"
#include "tokenizer.h"
#include "update.h"
#include "variable.h"
@ -2271,7 +2272,7 @@ void FixRigid::readfile(int which, double *vec,
double **array1, double **array2, double **array3,
imageint *ivec, int *inbody)
{
int j,nchunk,id,eofflag,xbox,ybox,zbox;
int nchunk,id,eofflag,xbox,ybox,zbox;
int nlines;
FILE *fp;
char *eof,*start,*next,*buf;
@ -2280,24 +2281,22 @@ void FixRigid::readfile(int which, double *vec,
if (me == 0) {
fp = fopen(inpfile,"r");
if (fp == nullptr)
error->one(FLERR,"Cannot open fix rigid file {}: {}",
inpfile,utils::getsyserror());
error->one(FLERR,"Cannot open fix rigid file {}: {}", inpfile,utils::getsyserror());
while (true) {
eof = fgets(line,MAXLINE,fp);
if (eof == nullptr) error->one(FLERR,"Unexpected end of fix rigid file");
start = &line[strspn(line," \t\n\v\f\r")];
if (*start != '\0' && *start != '#') break;
}
sscanf(line,"%d",&nlines);
nlines = utils::inumeric(FLERR, utils::trim(line), true, lmp);
}
MPI_Bcast(&nlines,1,MPI_INT,0,world);
if (nlines == 0) error->all(FLERR,"Fix rigid file has no lines");
// empty file with 0 lines is needed to trigger initial restart file generation
if (nlines == 0) return; //error->all(FLERR,"Fix rigid file has no lines");
char *buffer = new char[CHUNK*MAXLINE];
char **values = new char*[ATTRIBUTE_PERBODY];
int nread = 0;
while (nread < nlines) {
nchunk = MIN(nlines-nread,CHUNK);
@ -2322,58 +2321,59 @@ void FixRigid::readfile(int which, double *vec,
for (int i = 0; i < nchunk; i++) {
next = strchr(buf,'\n');
*next = '\0';
values[0] = strtok(buf," \t\n\r\f");
for (j = 1; j < nwords; j++)
values[j] = strtok(nullptr," \t\n\r\f");
try {
ValueTokenizer values(buf);
id = values.next_int();
if (rstyle == MOLECULE) {
if (id <= 0 || id > maxmol)
throw TokenizerException("invalid rigid body ID ", std::to_string(id));
id = mol2body[id];
} else id--;
id = atoi(values[0]);
if (rstyle == MOLECULE) {
if (id <= 0 || id > maxmol)
error->all(FLERR,"Invalid rigid body ID in fix rigid file");
id = mol2body[id];
} else id--;
if (id < 0 || id >= nbody)
throw TokenizerException("invalid_rigid body ID ", std::to_string(id+1));
if (id < 0 || id >= nbody)
error->all(FLERR,"Invalid rigid body ID in fix rigid file");
inbody[id] = 1;
inbody[id] = 1;
if (which == 0) {
vec[id] = atof(values[1]);
array1[id][0] = atof(values[2]);
array1[id][1] = atof(values[3]);
array1[id][2] = atof(values[4]);
array2[id][0] = atof(values[11]);
array2[id][1] = atof(values[12]);
array2[id][2] = atof(values[13]);
array3[id][0] = atof(values[14]);
array3[id][1] = atof(values[15]);
array3[id][2] = atof(values[16]);
xbox = atoi(values[17]);
ybox = atoi(values[18]);
zbox = atoi(values[19]);
ivec[id] = ((imageint) (xbox + IMGMAX) & IMGMASK) |
(((imageint) (ybox + IMGMAX) & IMGMASK) << IMGBITS) |
(((imageint) (zbox + IMGMAX) & IMGMASK) << IMG2BITS);
} else {
array1[id][0] = atof(values[5]);
array1[id][1] = atof(values[6]);
array1[id][2] = atof(values[7]);
array1[id][3] = atof(values[10]);
array1[id][4] = atof(values[9]);
array1[id][5] = atof(values[8]);
if (which == 0) {
vec[id] = values.next_double();
array1[id][0] = values.next_double();
array1[id][1] = values.next_double();
array1[id][2] = values.next_double();
values.skip(6);
array2[id][0] = values.next_double();
array2[id][1] = values.next_double();
array2[id][2] = values.next_double();
array3[id][0] = values.next_double();
array3[id][1] = values.next_double();
array3[id][2] = values.next_double();
xbox = values.next_int();
ybox = values.next_int();
zbox = values.next_int();
ivec[id] = ((imageint) (xbox + IMGMAX) & IMGMASK) |
(((imageint) (ybox + IMGMAX) & IMGMASK) << IMGBITS) |
(((imageint) (zbox + IMGMAX) & IMGMASK) << IMG2BITS);
} else {
values.skip(4);
array1[id][0] = values.next_double();
array1[id][1] = values.next_double();
array1[id][2] = values.next_double();
array1[id][5] = values.next_double();
array1[id][4] = values.next_double();
array1[id][3] = values.next_double();
}
} catch (TokenizerException &e) {
error->all(FLERR, "Invalid fix rigid file: {}", e.what());
}
buf = next + 1;
}
nread += nchunk;
}
if (me == 0) fclose(fp);
delete [] buffer;
delete [] values;
delete[] buffer;
}
/* ----------------------------------------------------------------------
@ -2389,11 +2389,9 @@ void FixRigid::write_restart_file(const char *file)
auto outfile = std::string(file) + ".rigid";
FILE *fp = fopen(outfile.c_str(),"w");
if (fp == nullptr)
error->one(FLERR,"Cannot open fix rigid restart file {}: {}",
outfile,utils::getsyserror());
error->one(FLERR,"Cannot open fix rigid restart file {}: {}",outfile,utils::getsyserror());
fmt::print(fp,"# fix rigid mass, COM, inertia tensor info for "
"{} bodies on timestep {}\n\n",nbody,update->ntimestep);
fmt::print(fp,"# fix rigid mass, COM, inertia tensor info for {} bodies on timestep {}\n\n",nbody,update->ntimestep);
fmt::print(fp,"{}\n",nbody);
// compute I tensor against xyz axes from diagonalized I and current quat
@ -2405,7 +2403,7 @@ void FixRigid::write_restart_file(const char *file)
int id;
for (int i = 0; i < nbody; i++) {
if (rstyle == SINGLE || rstyle == GROUP) id = i;
if (rstyle == SINGLE || rstyle == GROUP) id = i+1;
else id = body2mol[i];
MathExtra::col2mat(ex_space[i],ey_space[i],ez_space[i],p);
@ -2416,10 +2414,8 @@ void FixRigid::write_restart_file(const char *file)
ybox = (imagebody[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (imagebody[i] >> IMG2BITS) - IMGMAX;
fprintf(fp,"%d %-1.16e %-1.16e %-1.16e %-1.16e "
"%-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e "
"%-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e "
"%d %d %d\n",
fprintf(fp,"%d %.16g %.16g %.16g %.16g %.16g %.16g %.16g %.16g %.16g %.16g "
"%.16g %.16g %.16g %.16g %.16g %.16g %d %d %d\n",
id,masstotal[i],xcm[i][0],xcm[i][1],xcm[i][2],
ispace[0][0],ispace[1][1],ispace[2][2],
ispace[0][1],ispace[0][2],ispace[1][2],