Unverified Commit 43f6fa4b authored by Axel Kohlmeyer's avatar Axel Kohlmeyer Committed by GitHub
Browse files

Merge pull request #2136 from rbberger/refactor-reading 

Refactor value parsing code segments and add dump tests
parents d63f3d87 c7f8a6d1

src/dump_atom.cpp

+87 −0
Original line number Diff line number Diff line
@@ -166,8 +166,83 @@ void DumpAtom::write_data(int n, double *mybuf) 


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



void DumpAtom::format_magic_string_binary()

{

  // use negative ntimestep as marker for new format

  bigint fmtlen = strlen(MAGIC_STRING);

  bigint marker = -fmtlen;

  fwrite(&marker, sizeof(bigint), 1, 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_unit_style_binary()

{

  int len = 0;

  if (unit_flag && !unit_count) {

    ++unit_count;

    len = strlen(update->unit_style);

    fwrite(&len, sizeof(int), 1, fp);

    fwrite(update->unit_style, sizeof(char), len, fp);

  } else {

    fwrite(&len, sizeof(int), 1, fp);

  }

}



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



void DumpAtom::header_columns_binary()

{

  int len = strlen(columns);

  fwrite(&len, sizeof(int), 1, fp);

  fwrite(columns, sizeof(char), len, fp);

}



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



void DumpAtom::header_time_binary()

{

  char flag = time_flag ? 1 : 0;

  fwrite(&flag, sizeof(char), 1, fp);



  if (time_flag) {

    double t = compute_time();

    fwrite(&t, sizeof(double), 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);
@@ -179,6 +254,11 @@ 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);



  header_unit_style_binary();

  header_time_binary();

  header_columns_binary();



  if (multiproc) fwrite(&nclusterprocs,sizeof(int),1,fp);

  else fwrite(&nprocs,sizeof(int),1,fp);

}
@@ -187,6 +267,8 @@ void DumpAtom::header_binary(bigint ndump) 


void DumpAtom::header_binary_triclinic(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);
@@ -201,6 +283,11 @@ void DumpAtom::header_binary_triclinic(bigint ndump) 
  fwrite(&boxxz,sizeof(double),1,fp);

  fwrite(&boxyz,sizeof(double),1,fp);

  fwrite(&size_one,sizeof(int),1,fp);



  header_unit_style_binary();

  header_time_binary();

  header_columns_binary();



  if (multiproc) fwrite(&nclusterprocs,sizeof(int),1,fp);

  else fwrite(&nprocs,sizeof(int),1,fp);

}

src/dump_atom.h

+12 −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 +45,14 @@ class DumpAtom : public Dump { 
  int convert_string(int, double *);

  void write_data(int, double *);



  void header_format_binary();

  void header_unit_style_binary();

  void header_time_binary();

  void header_columns_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);

src/dump_custom.cpp

+89 −2
Original line number Diff line number Diff line
@@ -183,7 +183,7 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) : 
  columns[0] = '\0';

  for (int iarg = 0; iarg < nfield; iarg++) {

    strcat(columns,earg[iarg]);

    strcat(columns," ");

    if (iarg+1 < nfield) strcat(columns," ");

  }

}
@@ -302,7 +302,7 @@ void DumpCustom::init_style() 
      strcpy(vformat[i],ptr);

    }



    vformat[i] = strcat(vformat[i]," ");

    if (i+1 < size_one) vformat[i] = strcat(vformat[i]," ");

  }



  // setup boundary string
@@ -381,8 +381,83 @@ void DumpCustom::write_header(bigint ndump) 


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



void DumpCustom::format_magic_string_binary()

{

  // use negative ntimestep as marker for new format

  bigint fmtlen = strlen(MAGIC_STRING);

  bigint marker = -fmtlen;

  fwrite(&marker, sizeof(bigint), 1, fp);

  fwrite(MAGIC_STRING, sizeof(char), fmtlen, fp);

}



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



void DumpCustom::format_endian_binary()

{

  int endian = ENDIAN;

  fwrite(&endian, sizeof(int), 1, fp);

}



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



void DumpCustom::format_revision_binary()

{

  int revision = FORMAT_REVISION;

  fwrite(&revision, sizeof(int), 1, fp);

}



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



void DumpCustom::header_unit_style_binary()

{

  int len = 0;

  if (unit_flag && !unit_count) {

    ++unit_count;

    len = strlen(update->unit_style);

    fwrite(&len, sizeof(int), 1, fp);

    fwrite(update->unit_style, sizeof(char), len, fp);

  } else {

    fwrite(&len, sizeof(int), 1, fp);

  }

}



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



void DumpCustom::header_columns_binary()

{

  int len = strlen(columns);

  fwrite(&len, sizeof(int), 1, fp);

  fwrite(columns, sizeof(char), len, fp);

}



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



void DumpCustom::header_time_binary()

{

  char flag = time_flag ? 1 : 0;

  fwrite(&flag, sizeof(char), 1, fp);



  if (time_flag) {

    double t = compute_time();

    fwrite(&t, sizeof(double), 1, fp);

  }

}



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



void DumpCustom::header_format_binary()

{

  format_magic_string_binary();

  format_endian_binary();

  format_revision_binary();

}



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



void DumpCustom::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);
@@ -394,6 +469,11 @@ void DumpCustom::header_binary(bigint ndump) 
  fwrite(&boxzlo,sizeof(double),1,fp);

  fwrite(&boxzhi,sizeof(double),1,fp);

  fwrite(&size_one,sizeof(int),1,fp);



  header_unit_style_binary();

  header_time_binary();

  header_columns_binary();



  if (multiproc) fwrite(&nclusterprocs,sizeof(int),1,fp);

  else fwrite(&nprocs,sizeof(int),1,fp);

}
@@ -402,6 +482,8 @@ void DumpCustom::header_binary(bigint ndump) 


void DumpCustom::header_binary_triclinic(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);
@@ -416,6 +498,11 @@ void DumpCustom::header_binary_triclinic(bigint ndump) 
  fwrite(&boxxz,sizeof(double),1,fp);

  fwrite(&boxyz,sizeof(double),1,fp);

  fwrite(&size_one,sizeof(int),1,fp);



  header_unit_style_binary();

  header_time_binary();

  header_columns_binary();



  if (multiproc) fwrite(&nclusterprocs,sizeof(int),1,fp);

  else fwrite(&nprocs,sizeof(int),1,fp);

}

src/dump_custom.h

+12 −0
Original line number Diff line number Diff line
@@ -29,6 +29,10 @@ class DumpCustom : public Dump { 
  DumpCustom(class LAMMPS *, int, char **);

  virtual ~DumpCustom();



  const char * MAGIC_STRING = "DUMPCUSTOM";

  const int    FORMAT_REVISION = 0x0002;

  const int    ENDIAN = 0x0001;



 protected:

  int nevery;                // dump frequency for output

  int iregion;               // -1 if no region, else which region
@@ -107,6 +111,14 @@ class DumpCustom : public Dump { 
  int add_custom(char *, int);

  virtual int modify_param(int, char **);



  void header_format_binary();

  void header_unit_style_binary();

  void header_time_binary();

  void header_columns_binary();

  void format_magic_string_binary();

  void format_endian_binary();

  void format_revision_binary();



  typedef void (DumpCustom::*FnPtrHeader)(bigint);

  FnPtrHeader header_choice;           // ptr to write header functions

  void header_binary(bigint);

src/info.cpp

+20 −0
Original line number Diff line number Diff line
@@ -1243,6 +1243,26 @@ string Info::get_openmp_info() 
#endif

}



string Info::get_mpi_vendor() {

  #if defined(MPI_STUBS)

  return "MPI STUBS";

  #elif defined(OPEN_MPI)

  return "Open MPI";

  #elif defined(MPICH_NAME)

  return "MPICH";

  #elif defined(I_MPI_VERSION)

  return "Intel MPI";

  #elif defined(PLATFORM_MPI)

  return "Platform MPI";

  #elif defined(HP_MPI)

  return "HP MPI";

  #elif defined(MSMPI_VER)

  return "Microsoft MPI";

  #else

  return "Unknown";

  #endif

}



string Info::get_mpi_info(int &major, int &minor)

{

  int len;

CRA Git | Maintained and supported by SUSTech CRA and CCSE