Sync DumpAtom and binary2txt to generate the same (2ad9e06b) · Commits · 郑智淋 / lammps

src/dump_atom.cpp

+10 −0

Original line number	Diff line number	Diff line
		@@ -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);
		}

tools/binary2txt.cpp

+49 −9

Original line number	Diff line number	Diff line
		@@ -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;

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