--- trunk/OOPSE-1.0/libmdtools/SimSetup.cpp	2004/07/26 17:50:57	1415
+++ trunk/OOPSE-1.0/libmdtools/SimSetup.cpp	2004/08/09 14:50:35	1451
@@ -57,6 +57,28 @@ bool isDivisible(double dividend, double divisor){
     return false;  
 }
 
+string getPrefix(const string& str ){
+  string prefix;
+  string suffix;
+  int pos; 
+
+  pos = str.rfind(".");
+
+  if (pos >= 0) {
+     prefix = str.substr(0, pos);
+     suffix = str.substr(pos, str.size());
+
+     // leave .bass there in case we've reverted to old habits 
+     if (LowerCase(suffix) == ".md" || LowerCase(suffix) == ".bass")
+       return prefix;
+     else 
+       return str;
+     
+  } else 
+    return str;
+};
+
+
 SimSetup::SimSetup(){
   
   initSuspend = false;
@@ -74,6 +96,9 @@ SimSetup::~SimSetup(){
 }
 
 SimSetup::~SimSetup(){
+  // clean up the forcefield
+  the_ff->cleanMe();
+
   delete stamps;
   delete globals;
 }
@@ -92,6 +117,8 @@ void SimSetup::parseFile(char* fileName){
 #endif // is_mpi
 
     inFileName = fileName;
+
+    globals->initalize();
     set_interface_stamps(stamps, globals);
 
 #ifdef IS_MPI
@@ -122,7 +149,7 @@ void SimSetup::createSim(void){
 
 void SimSetup::createSim(void){
 
-  // gather all of the information from the Bass file
+  // gather all of the information from the meta-data file
 
   gatherInfo();
 
@@ -643,178 +670,9 @@ void SimSetup::makeMolecules(void){
   sprintf(checkPointMsg, "all molecules initialized succesfully");
   MPIcheckPoint();
 #endif // is_mpi
-
-}
-
-void SimSetup::initFromBass(void){
-  int i, j, k;
-  int n_cells;
-  double cellx, celly, cellz;
-  double temp1, temp2, temp3;
-  int n_per_extra;
-  int n_extra;
-  int have_extra, done;
-
-  double vel[3];
-  vel[0] = 0.0;
-  vel[1] = 0.0;
-  vel[2] = 0.0;
-
-  temp1 = (double) tot_nmol / 4.0;
-  temp2 = pow(temp1, (1.0 / 3.0));
-  temp3 = ceil(temp2);
-
-  have_extra = 0;
-  if (temp2 < temp3){
-    // we have a non-complete lattice
-    have_extra = 1;
-
-    n_cells = (int) temp3 - 1;
-    cellx = info[0].boxL[0] / temp3;
-    celly = info[0].boxL[1] / temp3;
-    cellz = info[0].boxL[2] / temp3;
-    n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
-    temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
-    n_per_extra = (int) ceil(temp1);
-
-    if (n_per_extra > 4){
-      sprintf(painCave.errMsg,
-              "SimSetup error. There has been an error in constructing"
-              " the non-complete lattice.\n");
-      painCave.isFatal = 1;
-      simError();
-    }
-  }
-  else{
-    n_cells = (int) temp3;
-    cellx = info[0].boxL[0] / temp3;
-    celly = info[0].boxL[1] / temp3;
-    cellz = info[0].boxL[2] / temp3;
-  }
-
-  current_mol = 0;
-  current_comp_mol = 0;
-  current_comp = 0;
-  current_atom_ndx = 0;
-
-  for (i = 0; i < n_cells ; i++){
-    for (j = 0; j < n_cells; j++){
-      for (k = 0; k < n_cells; k++){
-        makeElement(i * cellx, j * celly, k * cellz);
 
-        makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
-
-        makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
-
-        makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
-      }
-    }
-  }
-
-  if (have_extra){
-    done = 0;
-
-    int start_ndx;
-    for (i = 0; i < (n_cells + 1) && !done; i++){
-      for (j = 0; j < (n_cells + 1) && !done; j++){
-        if (i < n_cells){
-          if (j < n_cells){
-            start_ndx = n_cells;
-          }
-          else
-            start_ndx = 0;
-        }
-        else
-          start_ndx = 0;
-
-        for (k = start_ndx; k < (n_cells + 1) && !done; k++){
-          makeElement(i * cellx, j * celly, k * cellz);
-          done = (current_mol >= tot_nmol);
-
-          if (!done && n_per_extra > 1){
-            makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
-                        k * cellz);
-            done = (current_mol >= tot_nmol);
-          }
-
-          if (!done && n_per_extra > 2){
-            makeElement(i * cellx, j * celly + 0.5 * celly,
-                        k * cellz + 0.5 * cellz);
-            done = (current_mol >= tot_nmol);
-          }
-
-          if (!done && n_per_extra > 3){
-            makeElement(i * cellx + 0.5 * cellx, j * celly,
-                        k * cellz + 0.5 * cellz);
-            done = (current_mol >= tot_nmol);
-          }
-        }
-      }
-    }
-  }
-
-  for (i = 0; i < info[0].n_atoms; i++){
-    info[0].atoms[i]->setVel(vel);
-  }
 }
 
-void SimSetup::makeElement(double x, double y, double z){
-  int k;
-  AtomStamp* current_atom;
-  DirectionalAtom* dAtom;
-  double rotMat[3][3];
-  double pos[3];
-
-  for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
-    current_atom = comp_stamps[current_comp]->getAtom(k);
-    if (!current_atom->havePosition()){
-      sprintf(painCave.errMsg,
-              "SimSetup:initFromBass error.\n"
-              "\tComponent %s, atom %s does not have a position specified.\n"
-              "\tThe initialization routine is unable to give a start"
-              " position.\n",
-              comp_stamps[current_comp]->getID(), current_atom->getType());
-      painCave.isFatal = 1;
-      simError();
-    }
-
-    pos[0] = x + current_atom->getPosX();
-    pos[1] = y + current_atom->getPosY();
-    pos[2] = z + current_atom->getPosZ();
-
-    info[0].atoms[current_atom_ndx]->setPos(pos);
-
-    if (info[0].atoms[current_atom_ndx]->isDirectional()){
-      dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
-
-      rotMat[0][0] = 1.0;
-      rotMat[0][1] = 0.0;
-      rotMat[0][2] = 0.0;
-
-      rotMat[1][0] = 0.0;
-      rotMat[1][1] = 1.0;
-      rotMat[1][2] = 0.0;
-
-      rotMat[2][0] = 0.0;
-      rotMat[2][1] = 0.0;
-      rotMat[2][2] = 1.0;
-
-      dAtom->setA(rotMat);
-    }
-
-    current_atom_ndx++;
-  }
-
-  current_mol++;
-  current_comp_mol++;
-
-  if (current_comp_mol >= components_nmol[current_comp]){
-    current_comp_mol = 0;
-    current_comp++;
-  }
-}
-
-
 void SimSetup::gatherInfo(void){
   int i;
 
@@ -974,7 +832,6 @@ void SimSetup::gatherInfo(void){
       }        
     }
 
-    
     for (i=0; i < nInfo; i++) {
       
       // check for the temperature set flag
@@ -994,7 +851,7 @@ void SimSetup::gatherInfo(void){
           info[i].thermIntLambda = globals->getThermIntLambda();
           info[i].thermIntK = globals->getThermIntK();
           
-          Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
+          Restraints *myRestraint = new Restraints(info[i].thermIntLambda, info[i].thermIntK);
           info[i].restraint = myRestraint;
         }
         else {
@@ -1003,7 +860,7 @@ void SimSetup::gatherInfo(void){
                   "\tKeyword useSolidThermInt was set to 'true' but\n"
                   "\tthermodynamicIntegrationLambda (and/or\n"
                   "\tthermodynamicIntegrationK) was not specified.\n"
-                  "\tPlease provide a lambda value and k value in your .bass file.\n");
+                  "\tPlease provide a lambda value and k value in your meta-data file.\n");
           painCave.isFatal = 1;
           simError();    
         }
@@ -1012,12 +869,12 @@ void SimSetup::gatherInfo(void){
         if (globals->getUseSolidThermInt()) {
           sprintf( painCave.errMsg,
                    "SimSetup Warning: It appears that you have both solid and\n"
-                   "\tliquid thermodynamic integration activated in your .bass\n"
+                   "\tliquid thermodynamic integration activated in your meta-data\n"
                    "\tfile. To avoid confusion, specify only one technique in\n"
-                   "\tyour .bass file. Liquid-state thermodynamic integration\n"
+                   "\tyour meta-data file. Liquid-state thermodynamic integration\n"
                    "\twill be assumed for the current simulation. If this is not\n"
                    "\twhat you desire, set useSolidThermInt to 'true' and\n"
-                   "\tuseLiquidThermInt to 'false' in your .bass file.\n");
+                   "\tuseLiquidThermInt to 'false' in your meta-data file.\n");
           painCave.isFatal = 0;
           simError();
         }
@@ -1032,7 +889,7 @@ void SimSetup::gatherInfo(void){
                   "\tKeyword useLiquidThermInt was set to 'true' but\n"
                   "\tthermodynamicIntegrationLambda (and/or\n"
                   "\tthermodynamicIntegrationK) was not specified.\n"
-                  "\tPlease provide a lambda value and k value in your .bass file.\n");
+                  "\tPlease provide a lambda value and k value in your meta-data file.\n");
           painCave.isFatal = 1;
           simError();    
         }
@@ -1041,7 +898,7 @@ void SimSetup::gatherInfo(void){
         sprintf(painCave.errMsg,
                 "SimSetup Warning: If you want to use Thermodynamic\n"
                 "\tIntegration, set useSolidThermInt or useLiquidThermInt to\n"
-                "\t'true' in your .bass file.  These keywords are set to\n"
+                "\t'true' in your meta-data file.  These keywords are set to\n"
                 "\t'false' by default, so your lambda and/or k values are\n"
                 "\tbeing ignored.\n");
         painCave.isFatal = 0;
@@ -1136,7 +993,7 @@ void SimSetup::gatherInfo(void){
   }
   
 #ifdef IS_MPI
-  strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
+  strcpy(checkPointMsg, "Successfully gathered all information from meta-data file\n");
   MPIcheckPoint();
 #endif // is_mpi
 }
@@ -1273,8 +1130,6 @@ void SimSetup::finalInfoCheck(void){
   MPIcheckPoint();
 #endif // is_mpi
 
-  // clean up the forcefield
-  the_ff->cleanMe();
 }
   
 void SimSetup::initSystemCoords(void){
@@ -1305,7 +1160,7 @@ void SimSetup::initSystemCoords(void){
   }
   else{
     
-    // no init from bass
+    // no init from md file 
     
     sprintf(painCave.errMsg,
             "Cannot intialize a simulation without an initial configuration file.\n");
@@ -1323,109 +1178,21 @@ void SimSetup::makeOutNames(void){
 
 void SimSetup::makeOutNames(void){
   int k;
+  string prefix;
 
-
   for (k = 0; k < nInfo; k++){
 #ifdef IS_MPI
     if (worldRank == 0){
 #endif // is_mpi
-
-      if (globals->haveFinalConfig()){
-        strcpy(info[k].finalName, globals->getFinalConfig());
-      }
-      else{
-        strcpy(info[k].finalName, inFileName);
-        char* endTest;
-        int nameLength = strlen(info[k].finalName);
-        endTest = &(info[k].finalName[nameLength - 5]);
-        if (!strcmp(endTest, ".bass")){
-          strcpy(endTest, ".eor");
-        }
-        else if (!strcmp(endTest, ".BASS")){
-          strcpy(endTest, ".eor");
-        }
-        else{
-          endTest = &(info[k].finalName[nameLength - 4]);
-          if (!strcmp(endTest, ".bss")){
-            strcpy(endTest, ".eor");
-          }
-          else if (!strcmp(endTest, ".mdl")){
-            strcpy(endTest, ".eor");
-          }
-          else{
-            strcat(info[k].finalName, ".eor");
-          }
-        }
-      }
+      
+      if(globals->haveFinalConfig()) 
+	prefix = getPrefix(globals->getFinalConfig());   
+      else
+	prefix = getPrefix(inFileName);
 
-      // make the sample and status out names
-
-      strcpy(info[k].sampleName, inFileName);
-      char* endTest;
-      int nameLength = strlen(info[k].sampleName);
-      endTest = &(info[k].sampleName[nameLength - 5]);
-      if (!strcmp(endTest, ".bass")){
-        strcpy(endTest, ".dump");
-      }
-      else if (!strcmp(endTest, ".BASS")){
-        strcpy(endTest, ".dump");
-      }
-      else{
-        endTest = &(info[k].sampleName[nameLength - 4]);
-        if (!strcmp(endTest, ".bss")){
-          strcpy(endTest, ".dump");
-        }
-        else if (!strcmp(endTest, ".mdl")){
-          strcpy(endTest, ".dump");
-        }
-        else{
-          strcat(info[k].sampleName, ".dump");
-        }
-      }
-
-      strcpy(info[k].statusName, inFileName);
-      nameLength = strlen(info[k].statusName);
-      endTest = &(info[k].statusName[nameLength - 5]);
-      if (!strcmp(endTest, ".bass")){
-        strcpy(endTest, ".stat");
-      }
-      else if (!strcmp(endTest, ".BASS")){
-        strcpy(endTest, ".stat");
-      }
-      else{
-        endTest = &(info[k].statusName[nameLength - 4]);
-        if (!strcmp(endTest, ".bss")){
-          strcpy(endTest, ".stat");
-        }
-        else if (!strcmp(endTest, ".mdl")){
-          strcpy(endTest, ".stat");
-        }
-        else{
-          strcat(info[k].statusName, ".stat");
-        }
-      }
-
-      strcpy(info[k].rawPotName, inFileName);
-      nameLength = strlen(info[k].rawPotName);
-      endTest = &(info[k].rawPotName[nameLength - 5]);
-      if (!strcmp(endTest, ".bass")){
-        strcpy(endTest, ".raw");
-      }
-      else if (!strcmp(endTest, ".BASS")){
-        strcpy(endTest, ".raw");
-      }
-      else{
-        endTest = &(info[k].rawPotName[nameLength - 4]);
-        if (!strcmp(endTest, ".bss")){
-          strcpy(endTest, ".raw");
-        }
-        else if (!strcmp(endTest, ".mdl")){
-          strcpy(endTest, ".raw");
-        }
-        else{
-          strcat(info[k].rawPotName, ".raw");
-        }
-      }
+      info[k].finalName = prefix + ".eor";	
+      info[k].sampleName = prefix + ".dump";
+      info[k].statusName = prefix + ".stat";
 
 #ifdef IS_MPI
 
@@ -1853,7 +1620,7 @@ void SimSetup::makeIntegrator(void){
         else{
           sprintf(painCave.errMsg,
                   "SimSetup error: If you use a constant pressure\n"
-                  "\tensemble, you must set targetPressure in the BASS file.\n");
+                  "\tensemble, you must set targetPressure in the meta-data file.\n");
           painCave.isFatal = 1;
           simError();
         }
@@ -1904,7 +1671,7 @@ void SimSetup::makeIntegrator(void){
         else{
           sprintf(painCave.errMsg,
                   "SimSetup error: If you use a constant pressure\n"
-                  "\tensemble, you must set targetPressure in the BASS file.\n");
+                  "\tensemble, you must set targetPressure in the meta-data file.\n");
           painCave.isFatal = 1;
           simError();
         }    
@@ -1957,7 +1724,7 @@ void SimSetup::makeIntegrator(void){
         else{
           sprintf(painCave.errMsg,
                   "SimSetup error: If you use a constant pressure\n"
-                  "\tensemble, you must set targetPressure in the BASS file.\n");
+                  "\tensemble, you must set targetPressure in the meta-data file.\n");
           painCave.isFatal = 1;
           simError();
         }