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Sync DumpAtom and binary2txt to generate the same 

Modifies the binary dump atom format to include columns information.
binary2txt showcases how to detect the new format by checking for
negative ntimestep values. It increases the binary file size
16 bytes per timestep.
This commit is contained in:
Richard Berger 2020-08-11 14:58:36 -04:00
parent e3a1fd7c02
commit 2ad9e06bac
No known key found for this signature in database
GPG Key ID: A9E83994E0BA0CAB
2 changed files with 59 additions and 9 deletions
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10
src/dump_atom.cpp
View File

@ -168,6 +168,11 @@ void DumpAtom::write_data(int n, double *mybuf)
void DumpAtom::header_binary(bigint ndump)
{
// use negative ntimestep as marker for new format
bigint fmtlen = strlen("DUMPATOM");
bigint marker = -fmtlen;
fwrite(&marker,sizeof(bigint),1,fp);
fwrite("DUMPATOM",sizeof(char),fmtlen,fp);
fwrite(&update->ntimestep,sizeof(bigint),1,fp);
fwrite(&ndump,sizeof(bigint),1,fp);
fwrite(&domain->triclinic,sizeof(int),1,fp);
@ -179,6 +184,11 @@ void DumpAtom::header_binary(bigint ndump)
fwrite(&boxzlo,sizeof(double),1,fp);
fwrite(&boxzhi,sizeof(double),1,fp);
fwrite(&size_one,sizeof(int),1,fp);
int len = strlen(columns);
fwrite(&len, sizeof(int), 1, fp);
fwrite(columns, sizeof(char), len, fp);
if (multiproc) fwrite(&nclusterprocs,sizeof(int),1,fp);
else fwrite(&nprocs,sizeof(int),1,fp);
}

58
tools/binary2txt.cpp
View File

@ -90,6 +90,11 @@ int main(int narg, char **arg)
FILE *fptxt = fopen(filetxt,"w");
delete [] filetxt;
// detect newer format
char * formatname = nullptr;
char * columns = nullptr;
// loop over snapshots in file
while (1) {
@ -104,6 +109,20 @@ int main(int narg, char **arg)
break;
}
// detect newer format
if (ntimestep < 0) {
// first bigint encodes negative format name length
bigint formatlen = -ntimestep;
delete [] formatname;
formatname = new char[formatlen + 1];
fread(formatname, sizeof(char), formatlen, fp);
formatname[formatlen] = '\0';
// read the real ntimestep
fread(&ntimestep,sizeof(bigint),1,fp);
}
fread(&natoms,sizeof(bigint),1,fp);
fread(&triclinic,sizeof(int),1,fp);
fread(&boundary[0][0],6*sizeof(int),1,fp);
@ -119,6 +138,17 @@ int main(int narg, char **arg)
fread(&yz,sizeof(double),1,fp);
}
fread(&size_one,sizeof(int),1,fp);
if (formatname) {
// newer format includes columns string
int len = 0;
fread(&len, sizeof(int), 1, fp);
delete [] columns;
columns = new char[len+1];
fread(columns, sizeof(char), len, fp);
columns[len+1] = '\0';
}
fread(&nchunk,sizeof(int),1,fp);
fprintf(fptxt,"ITEM: TIMESTEP\n");
@ -140,18 +170,20 @@ int main(int narg, char **arg)
if (!triclinic) {
fprintf(fptxt,"ITEM: BOX BOUNDS %s\n",boundstr);
fprintf(fptxt,"%g %g\n",xlo,xhi);
fprintf(fptxt,"%g %g\n",ylo,yhi);
fprintf(fptxt,"%g %g\n",zlo,zhi);
fprintf(fptxt,"%-1.16e %-1.16e\n",xlo,xhi);
fprintf(fptxt,"%-1.16e %-1.16e\n",ylo,yhi);
fprintf(fptxt,"%-1.16e %-1.16e\n",zlo,zhi);
} else {
fprintf(fptxt,"ITEM: BOX BOUNDS %s xy xz yz\n",boundstr);
fprintf(fptxt,"%g %g %g\n",xlo,xhi,xy);
fprintf(fptxt,"%g %g %g\n",ylo,yhi,xz);
fprintf(fptxt,"%g %g %g\n",zlo,zhi,yz);
fprintf(fptxt,"%-1.16e %-1.16e %-1.16e\n",xlo,xhi,xy);
fprintf(fptxt,"%-1.16e %-1.16e %-1.16e\n",ylo,yhi,xz);
fprintf(fptxt,"%-1.16e %-1.16e %-1.16e\n",zlo,zhi,yz);
}
fprintf(fptxt,"ITEM: ATOMS\n");
if (columns)
fprintf(fptxt,"ITEM: ATOMS %s\n", columns);
else
fprintf(fptxt,"ITEM: ATOMS\n");
// loop over processor chunks in file
@ -172,7 +204,13 @@ int main(int narg, char **arg)
n /= size_one;
m = 0;
for (j = 0; j < n; j++) {
for (k = 0; k < size_one; k++) fprintf(fptxt,"%g ",buf[m++]);
for (k = 0; k < size_one; k++) {
if(k+1 < size_one) {
fprintf(fptxt,"%g ",buf[m++]);
} else {
fprintf(fptxt,"%g",buf[m++]);
}
}
fprintf(fptxt,"\n");
}
}
@ -181,6 +219,8 @@ int main(int narg, char **arg)
fflush(stdout);
}
printf("\n");
delete [] columns;
delete [] formatname;
}
if (buf) delete [] buf;