Extends header of new binary format of dump atom (560c29a0) · Commits · 郑智淋 / lammps

src/dump_atom.cpp

+36 −9

Original line number	Diff line number	Diff line
		@@ -166,13 +166,44 @@ void DumpAtom::write_data(int n, double *mybuf)

		/* ---------------------------------------------------------------------- */

		void DumpAtom::header_binary(bigint ndump)
		void DumpAtom::format_magic_string_binary()
		{
		// use negative ntimestep as marker for new format
		bigint fmtlen = strlen("DUMPATOM");
		bigint fmtlen = strlen(MAGIC_STRING);
		bigint marker = -fmtlen;
		fwrite(&marker, sizeof(bigint), 1, fp);
		fwrite("DUMPATOM",sizeof(char),fmtlen,fp);
		fwrite(MAGIC_STRING, sizeof(char), fmtlen, fp);
		}

		/* ---------------------------------------------------------------------- */

		void DumpAtom::format_endian_binary()
		{
		int endian = ENDIAN;
		fwrite(&endian, sizeof(int), 1, fp);
		}
		/* ---------------------------------------------------------------------- */

		void DumpAtom::format_revision_binary()
		{
		int revision = FORMAT_REVISION;
		fwrite(&revision, sizeof(int), 1, fp);
		}

		/* ---------------------------------------------------------------------- */

		void DumpAtom::header_format_binary()
		{
		format_magic_string_binary();
		format_endian_binary();
		format_revision_binary();
		}

		/* ---------------------------------------------------------------------- */

		void DumpAtom::header_binary(bigint ndump)
		{
		header_format_binary();
		fwrite(&update->ntimestep,sizeof(bigint),1,fp);
		fwrite(&ndump,sizeof(bigint),1,fp);
		fwrite(&domain->triclinic,sizeof(int),1,fp);
		@@ -197,11 +228,7 @@ void DumpAtom::header_binary(bigint ndump)

		void DumpAtom::header_binary_triclinic(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);
		header_format_binary();
		fwrite(&update->ntimestep,sizeof(bigint),1,fp);
		fwrite(&ndump,sizeof(bigint),1,fp);
		fwrite(&domain->triclinic,sizeof(int),1,fp);

src/dump_atom.h

+9 −0

Original line number	Diff line number	Diff line
		@@ -28,6 +28,10 @@ class DumpAtom : public Dump {
		public:
		DumpAtom(LAMMPS , int, char*);

		const char * MAGIC_STRING = "DUMPATOM";
		const int FORMAT_REVISION = 0x0002;
		const int ENDIAN = 0x0001;

		protected:
		int scale_flag; // 1 if atom coords are scaled, 0 if no
		int image_flag; // 1 if append box count to atom coords, 0 if no
		@@ -41,6 +45,11 @@ class DumpAtom : public Dump {
		int convert_string(int, double *);
		void write_data(int, double *);

		void header_format_binary();
		void format_magic_string_binary();
		void format_endian_binary();
		void format_revision_binary();

		typedef void (DumpAtom::*FnPtrHeader)(bigint);
		FnPtrHeader header_choice; // ptr to write header functions
		void header_binary(bigint);

tools/binary2txt.cpp

+16 −8

Original line number	Diff line number	Diff line
		@@ -91,13 +91,15 @@ int main(int narg, char **arg)
		delete [] filetxt;

		// detect newer format
		char * formatname = nullptr;
		char * magic_string = nullptr;
		char * columns = nullptr;


		// loop over snapshots in file

		while (1) {
		int endian = 0x0001;
		int revision = 0x0001;

		fread(&ntimestep,sizeof(bigint),1,fp);

		@@ -112,12 +114,18 @@ int main(int narg, char **arg)
		// detect newer format
		if (ntimestep < 0) {
		// first bigint encodes negative format name length
		bigint formatlen = -ntimestep;
		bigint magic_string_len = -ntimestep;

		delete [] formatname;
		formatname = new char[formatlen + 1];
		fread(formatname, sizeof(char), formatlen, fp);
		formatname[formatlen] = '\0';
		delete [] magic_string;
		magic_string = new char[magic_string_len + 1];
		fread(magic_string, sizeof(char), magic_string_len, fp);
		magic_string[magic_string_len] = '\0';

		// read endian flag
		fread(&endian, sizeof(int), 1, fp);

		// read revision number
		fread(&revision, sizeof(int), 1, fp);

		// read the real ntimestep
		fread(&ntimestep,sizeof(bigint),1,fp);
		@@ -139,7 +147,7 @@ int main(int narg, char **arg)
		}
		fread(&size_one,sizeof(int),1,fp);

		if (formatname) {
		if (magic_string && revision > 0x0001) {
		// newer format includes columns string
		int len = 0;
		fread(&len, sizeof(int), 1, fp);
		@@ -220,7 +228,7 @@ int main(int narg, char **arg)
		}
		printf("\n");
		delete [] columns;
		delete [] formatname;
		delete [] magic_string;
		}

		if (buf) delete [] buf;

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