[ViewVC] Diff of: group/trunk/mdtools/md_code/InitializeFromFile.cpp

Comparing trunk/mdtools/md_code/InitializeFromFile.cpp (file contents):
Revision 205 by mmeineke, Thu Oct 31 21:20:49 2002 UTC vs.
Revision 206 by chuckv, Thu Dec 12 21:21:59 2002 UTC

+InitializeFromFile :: InitializeFromFile( char *in_name ){
-+
+#ifdef IS_MPI
-+
+  if (worldRank == 0) {
-+
+#endif
+  c_in_file = fopen(in_name, "r");
+  if(c_in_file == NULL){
+  strcpy( c_in_name, in_name);
-+
+#ifdef IS_MPI
-+
+  }
-+
+ strcpy( checkPointMsg, "Infile opened for reading successfully." );
-+
+  MPIcheckPoint();
-+
+#endif
+  return;
+InitializeFromFile :: ~InitializeFromFile( ){
-<
->
+#ifdef IS_MPI
->
+  if (worldRank == 0) {
->
+#endif
+  int error;
+  error = fclose( c_in_file );
+  if( error ){
+             "Error closing %s\n", c_in_name );
+    simError();
-+
+#ifdef IS_MPI
-+
+  }
-+
+  strcpy( checkPointMsg, "Infile closed successfully." );
-+
+  MPIcheckPoint();
-+
+#endif
-+
+  return;
-<
+void InitializeFromFile :: read_xyz( SimInfo* entry_plug ){
->
+void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){
+  int i; // loop counter
+  int n_atoms; // the number of atoms
+  char read_buffer[2000]; //the line buffer for reading
-+
+#ifdef IS_MPI
-+
+  char send_buffer[2000];
-+
+#endif
-+
+  char *eof_test; // ptr to see when we reach the end of the file
+  char *foo; // the pointer to the current string token
+  double jx, jy, jz; // angular velocity placeholders;
+  double qSqr, qLength; // needed to normalize the quaternion vector.
-+
+  entry_plug = the_entry_plug
-+
-+
-+
+#ifndef IS_MPI
+  eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
+  if( eof_test == NULL ){
+    std::cerr << "error reading 1st line of" << c_in_name << "\n";
+    atoms[i]->set_vz( vz );
-+
-+
-+
+  // MPI Section of code..........
-+
+#else //IS_MPI
-+
-+
-+
-+
-+
+  if (worldRank == 0) {
-+
+    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
-+
+    if( eof_test == NULL ){
-+
+      sprintf( painCave.errMsg,
-+
+               "Error reading 1st line of %d \n ",c_in_name);
-+
+      painCave.isFatal = 1;
-+
+      simError();
-+
+    }
-+
-+
+    (void)sscanf(read_buffer, "%d", &n_atoms);
-+
-+
+    Atom **atoms = entry_plug->atoms;
-+
+    DirectionalAtom* dAtom;
-+
-+
+    if( n_atoms != entry_plug->n_atoms ){
-+
+      sprintf( painCave.errMsg,
-+
+               "Initialize from File error. %s n_atoms, %d, "
-+
+               "does not match the BASS file's n_atoms, %d.\n",
-+
+               c_in_name, n_atoms, entry_plug->n_atoms );
-+
+      painCave.isFatal = 1;
-+
+      simError();
-+
+    }
-+
-+
+    //read and toss the comment line
-+
-+
+    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
-+
+    if(eof_test == NULL){
-+
+      sprintf( painCave.errMsg,
-+
+               "error in reading commment in %s\n", c_in_name);
-+
+      painCave.isFatal = 1;
-+
+      simError();
-+
+    }
-+
+  }
-+
+  for( i=0; i < n_atoms; i++){
-+
-+
+    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
-+
+    if(eof_test == NULL){
-+
+      sprintf(painCave.errMsg,
-+
+              "error in reading file %s\n"
-+
+              "natoms  = %d; index = %d\n"
-+
+              "error reading the line from the file.\n",
-+
+              c_in_name, n_atoms, i );
-+
+      painCave.isFatal = 1;
-+
+      simError();
-+
+    }
-+
-+
+    foo = strtok(read_buffer, " ,;\t");
-+
-+
+    // check the atom name to the current atom
-+
-+
+    if( strcmp( foo, atoms[i]->getType() ) ){
-+
+      sprintf( painCave.errMsg,
-+
+               "Initialize from file error. Atom %s at index %d "
-+
+               "in file %s does not"
-+
+               " match the BASS atom %s.\n",
-+
+               foo, i, c_in_name, atoms[i]->getType() );
-+
+      painCave.isFatal = 1;
-+
+      simError();
-+
+    }
-+
-+
+    // get the positions
-+
-+
+    foo = strtok(NULL, " ,;\t");
-+
+    if(foo == NULL){
-+
+      sprintf( painCave.errMsg,
-+
+               "error in reading postition x from %s\n"
-+
+               "natoms  = %d, index = %d\n",
-+
+               c_in_name, n_atoms, i );
-+
+      painCave.isFatal = 1;
-+
+      simError();
-+
+    }
-+
+    (void)sscanf( foo, "%lf", &rx );
-+
-+
+    foo = strtok(NULL, " ,;\t");
-+
+    if(foo == NULL){
-+
+      sprintf( painCave.errMsg,
-+
+               "error in reading postition y from %s\n"
-+
+               "natoms  = %d, index = %d\n",
-+
+               c_in_name, n_atoms, i );
-+
+      painCave.isFatal = 1;
-+
+      simError();
-+
+    }
-+
+    (void)sscanf( foo, "%lf", &ry );
-+
-+
+    foo = strtok(NULL, " ,;\t");
-+
+    if(foo == NULL){
-+
+      sprintf( painCave.errMsg,
-+
+               "error in reading postition z from %s\n"
-+
+               "natoms  = %d, index = %d\n",
-+
+               c_in_name, n_atoms, i );
-+
+      painCave.isFatal = 1;
-+
+      simError();
-+
+    }
-+
+    (void)sscanf( foo, "%lf", &rz );
-+
-+
+    // get the velocities
-+
-+
+    foo = strtok(NULL, " ,;\t");
-+
+    if(foo == NULL){
-+
+      sprintf( painCave.errMsg,
-+
+               "error in reading velocity x from %s\n"
-+
+               "natoms  = %d, index = %d\n",
-+
+               c_in_name, n_atoms, i );
-+
+      painCave.isFatal = 1;
-+
+      simError();
-+
+    }
-+
+    (void)sscanf( foo, "%lf", &vx );
-+
-+
+    foo = strtok(NULL, " ,;\t");
-+
+    if(foo == NULL){
-+
+      sprintf( painCave.errMsg,
-+
+               "error in reading velocity y from %s\n"
-+
+               "natoms  = %d, index = %d\n",
-+
+               c_in_name, n_atoms, i );
-+
+      painCave.isFatal = 1;
-+
+      simError();
-+
+    }
-+
+    (void)sscanf( foo, "%lf", &vy );
-+
-+
+    foo = strtok(NULL, " ,;\t");
-+
+    if(foo == NULL){
-+
+      sprintf( painCave.errMsg,
-+
+               "error in reading velocity z from %s\n"
-+
+               "natoms  = %d, index = %d\n",
-+
+               c_in_name, n_atoms, i );
-+
+      painCave.isFatal = 1;
-+
+      simError();
-+
+    }
-+
+    (void)sscanf( foo, "%lf", &vz );
-+
-+
-+
+    // get the quaternions
-+
-+
+    if( atoms[i]->isDirectional() ){
-+
-+
+      foo = strtok(NULL, " ,;\t");
-+
+      if(foo == NULL){
-+
+        sprintf(painCave.errMsg,
-+
+                "error in reading quaternion 0 from %s\n"
-+
+                "natoms  = %d, index = %d\n",
-+
+                c_in_name, n_atoms, i );
-+
+        painCave.isFatal = 1;
-+
+        simError();
-+
+      }
-+
+      (void)sscanf( foo, "%lf", &q[0] );
-+
-+
+      foo = strtok(NULL, " ,;\t");
-+
+      if(foo == NULL){
-+
+        sprintf( painCave.errMsg,
-+
+                 "error in reading quaternion 1 from %s\n"
-+
+                 "natoms  = %d, index = %d\n",
-+
+                 c_in_name, n_atoms, i );
-+
+        painCave.isFatal = 1;
-+
+        simError();
-+
+      }
-+
+      (void)sscanf( foo, "%lf", &q[1] );
-+
-+
+      foo = strtok(NULL, " ,;\t");
-+
+      if(foo == NULL){
-+
+        sprintf( painCave.errMsg,
-+
+                 "error in reading quaternion 2 from %s\n"
-+
+                 "natoms  = %d, index = %d\n",
-+
+                 c_in_name, n_atoms, i );
-+
+        painCave.isFatal = 1;
-+
+        simError();
-+
+      }
-+
+      (void)sscanf( foo, "%lf", &q[2] );
-+
-+
+      foo = strtok(NULL, " ,;\t");
-+
+      if(foo == NULL){
-+
+        sprintf( painCave.errMsg,
-+
+                 "error in reading quaternion 3 from %s\n"
-+
+                 "natoms  = %d, index = %d\n",
-+
+                 c_in_name, n_atoms, i );
-+
+        painCave.isFatal = 1;
-+
+        simError();
-+
+      }
-+
+      (void)sscanf( foo, "%lf", &q[3] );
-+
-+
+      // get the angular velocities
-+
-+
+      foo = strtok(NULL, " ,;\t");
-+
+      if(foo == NULL){
-+
+        sprintf( painCave.errMsg,
-+
+                 "error in reading angular momentum jx from %s\n"
-+
+                 "natoms  = %d, index = %d\n",
-+
+                 c_in_name, n_atoms, i );
-+
+        painCave.isFatal = 1;
-+
+        simError();
-+
+      }
-+
+      (void)sscanf( foo, "%lf", &jx );
-+
-+
+      foo = strtok(NULL, " ,;\t");
-+
+      if(foo == NULL){
-+
+        sprintf( painCave.errMsg,
-+
+                 "error in reading angular momentum jy from %s\n"
-+
+                 "natoms  = %d, index = %d\n",
-+
+                 c_in_name, n_atoms, i );
-+
+        painCave.isFatal = 1;
-+
+        simError();
-+
+      }
-+
+      (void)sscanf( foo, "%lf", &jy );
-+
-+
+      foo = strtok(NULL, " ,;\t");
-+
+      if(foo == NULL){
-+
+        sprintf( painCave.errMsg,
-+
+                 "error in reading angular momentum jz from %s\n"
-+
+                 "natoms  = %d, index = %d\n",
-+
+                 c_in_name, n_atoms, i );
-+
+        painCave.isFatal = 1;
-+
+        simError();
-+
+      }
-+
+      (void)sscanf( foo, "%lf", &jz );
-+
-+
+      dAtom = ( DirectionalAtom* )atoms[i];
-+
-+
+      // check that the quaternion vector is normalized
-+
-+
+      qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
-+
-+
+      qLength = sqrt( qSqr );
-+
+      q[0] = q[0] / qLength;
-+
+      q[1] = q[1] / qLength;
-+
+      q[2] = q[2] / qLength;
-+
+      q[3] = q[3] / qLength;
-+
-+
+      dAtom->setQ( q );
-+
-+
+      // add the angular velocities
-+
-+
+      dAtom->setJx( jx );
-+
+      dAtom->setJy( jy );
-+
+      dAtom->setJz( jz );
-+
+    }
-+
-+
+    // add the positions and velocities to the atom
-+
-+
+    atoms[i]->setX( rx );
-+
+    atoms[i]->setY( ry );
-+
+    atoms[i]->setZ( rz );
-+
-+
+    atoms[i]->set_vx( vx );
-+
+    atoms[i]->set_vy( vy );
-+
+    atoms[i]->set_vz( vz );
-+
-+
+  }
-+
+#endif
-+
-+
+char* IntitializeFromFile::parseDumpLine(char* readLine);

Diff Legend

-–
+Removed lines
-+
+Added lines
-<
+Changed lines
->
+Changed lines

Comparing trunk/mdtools/md_code/InitializeFromFile.cpp (file contents): Revision 205 by mmeineke, Thu Oct 31 21:20:49 2002 UTC vs. Revision 206 by chuckv, Thu Dec 12 21:21:59 2002 UTC

Diff Legend

Comparing trunk/mdtools/md_code/InitializeFromFile.cpp (file contents):
Revision 205 by mmeineke, Thu Oct 31 21:20:49 2002 UTC vs.
Revision 206 by chuckv, Thu Dec 12 21:21:59 2002 UTC