[ViewVC] Diff of: group/trunk/OOPSE/utils/sysBuild.cpp

Comparing trunk/OOPSE/utils/sysBuild.cpp (file contents):
Revision 495 by mmeineke, Mon Apr 14 19:52:00 2003 UTC vs.
Revision 598 by chuckv, Mon Jul 14 21:35:45 2003 UTC

-+
+#include <cstdlib>
+#include <cstdio>
+#include <cstring>
-+
+#include <cmath>
-–
+#include "simError.h"
-+
+#include "parse_me.h"
-+
+#include "MakeStamps.hpp"
-+
+#include "Globals.hpp"
-+
+#include "SimInfo.hpp"
-<
+// quick case asignments
->
+#include "sysBuild.hpp"
->
+#include "bilayerSys.hpp"
->
+#include "nanoBuilder.hpp"
-<
+#define BILAYER 1
->
+// this routine is defined in BASS_interface.cpp
->
+extern void set_interface_stamps( MakeStamps* ms, Globals* g );
-+
+// case asignments
-+
+#define BILAYER 1
-+
+#define NANOPARTICLE 2
-+
+char* program_name;
-+
+bassInfo bsInfo;
+void usage(void);
+  char current_flag;
+  char* out_prefix;
+  char* in_name;
-+
+  char* id;
-+
-+
+  includeLinked* headInc;
-+
+  includeLinked* prevInc;
-+
+  includeLinked* currInc;
-<
+  // initialize simError
-<
+  initSimError();
->
+  MakeStamps* the_stamps = NULL;
->
+  Globals* the_globals = NULL;
->
+  Component** the_components = NULL;
->
+  LinkedMolStamp* headStamp = NULL;
->
+  LinkedMolStamp* currStamp;
-+
+  // initialize all functions and variables
-<
+  program_name = argv[0]; /*save the program name in case we need it*/
->
+  initSimError();
->
+  program_name = argv[0];
+  sysType = -1;
+  have_prefix = 0;
+  isRandom = 0;
+  in_name = NULL;
-+
+  headInc = NULL;
-+
-+
+  bsInfo.includes = NULL;
-+
+  bsInfo.componentsNmol = NULL;
-+
+  bsInfo.compStamps = NULL;
-+
+  bsInfo.havePressure = 0;
-+
+  bsInfo.haveTauBarostat = 0;
-+
+  bsInfo.haveTauThermostat = 0;
-+
+  bsInfo.haveQmass = 0;
-+
-+
+  headStamp = new LinkedMolStamp();
-+
+  the_stamps = new MakeStamps();
-+
+  the_globals = new Globals();
-+
+  set_interface_stamps( the_stamps, the_globals );
-+
-+
+  // parse command line arguments
-+
+  for( i = 1; i < argc; i++){
+    if(argv[i][0] =='-'){
+            simError();
+            usage();
-+
+          sysType = BILAYER;
-+
-+
+          i++;
-+
+          if( i>=argc ){
-+
+            sprintf( painCave.errMsg,
-+
+                     "\n"
-+
+                     "not enough arguments for bilayer\n");
-+
+            painCave.isFatal = 0;
-+
+            simError();
-+
+            usage();
-+
+          }
-+
+          strcpy( bsInfo.lipidName, argv[i] );
-+
-+
+          i++;
-+
+          if( i>=argc ){
-+
+            sprintf( painCave.errMsg,
-+
+                     "\n"
-+
+                     "not enough arguments for bilayer\n");
-+
+            painCave.isFatal = 0;
-+
+            simError();
-+
+            usage();
-+
+          }
-+
+          strcpy( bsInfo.waterName, argv[i] );
-+
+        else{
+          usage();
-+
+      else if( !strcmp( argv[i], "--nanoparticle" ) ){
-+
+        if( sysType > 0 ){
-+
+            sprintf( painCave.errMsg,
-+
+                     "You cannot specify more than one system to build.\n" );
-+
+            painCave.isFatal = 0;
-+
+            simError();
-+
+            usage();
-+
+          }
-+
-+
+          sysType = NANOPARTICLE;
-+
-+
+          i++;
-+
+          if( i>=argc ){
-+
+            sprintf( painCave.errMsg,
-+
+                     "\n"
-+
+                     "not enough arguments for nanoparticle\n");
-+
+            painCave.isFatal = 0;
-+
+            simError();
-+
+            usage();
-+
+          }
-+
+          strcpy( bsInfo.coreName, argv[i] );
-+
-+
+          i++;
-+
+          if( i>=argc ){
-+
+            sprintf( painCave.errMsg,
-+
+                     "\n"
-+
+                     "not enough arguments for nanoparticle\n");
-+
+            painCave.isFatal = 0;
-+
+            simError();
-+
+            usage();
-+
+          }
-+
+          strcpy( bsInfo.shellName, argv[i] );
-+
-+
+        }
-+
-+
+        else{
-+
+          sprintf( painCave.errMsg,
-+
+                   "Invalid option \"%s\"\n", argv[i] );
-+
+          painCave.isFatal = 0;
-+
+          simError();
-+
+          usage();
-+
+        }
-+
+      }
+      else{
+            done = 1;
+            break;
-+
+          case 'I':
-+
+            // -I <include> => the include file.
-+
-+
+            i++;
-+
+            if( headInc == NULL ){
-+
+              headInc = new includeLinked;
-+
+              headInc->next = NULL;
-+
+              strcpy( headInc->name, argv[i] );
-+
+            }
-+
+            else{
-+
+              prevInc = headInc;
-+
+              currInc = headInc->next;
-+
+              while( currInc != NULL ){
-+
+                prevInc = currInc;
-+
+                currInc = prevInc->next;
-+
+              }
-+
+              currInc = new includeLinked;
-+
+              currInc->next = NULL;
-+
+              strcpy( currInc->name, argv[i] );
-+
+              prevInc->next = currInc;
-+
+            }
-+
-+
+            done = 1;
-+
+            break;
-+
+          case 'h':
+            // -h => give the usage
+          default:
+            sprintf(painCave.errMsg,
-<
+                    "Bad option \"-%s\"\n", current_flag);
->
+                    "Bad option \"-%c\"\n", current_flag);
+            painCave.isFatal = 0;
+            simError();
+            usage();
+  if(in_name == NULL){
-+
+    sprintf( painCave.errMsg,
-+
+             "No input bass file was specified.\n");
-+
+    painCave.isFatal = 0;
-+
+    simError();
+    usage();
-+
-+
+  if( sysType < 0 ){
-+
+    sprintf( painCave.errMsg,
-+
+             "No system type was specified.\n");
-+
+    painCave.isFatal = 0;
-+
+    simError();
-+
+    usage();
-+
+  }
-+
+  // if no output prefix is given default to "donkey".
-+
-+
+  if( !have_prefix ){
-+
+    out_prefix = strdup( "donkey" );
-+
+  }
-+
+  // set command line info into the bassInfo struct
-+
+  bsInfo.outPrefix = out_prefix;
-+
+  bsInfo.includes = headInc;
-+
-+
+  // open and parse the bass file.
-+
-+
+  set_interface_stamps( the_stamps, the_globals );
-+
+  yacc_BASS( in_name );
-+
-+
+  // set the easy ones first
-+
+  bsInfo.targetTemp = the_globals->getTargetTemp();
-+
+  bsInfo.dt = the_globals->getDt();
-+
+  bsInfo.runTime = the_globals->getRunTime();
-+
-+
+  // get the ones we know are there, yet still may need some work.
-+
+  bsInfo.nComponents = the_globals->getNComponents();
-+
+  strcpy( bsInfo.forceField, the_globals->getForceField() );
-+
-+
+  // get the ensemble:
-+
+  strcpy( bsInfo.ensemble, the_globals->getEnsemble() );
-+
+  if( !strcasecmp( bsInfo.ensemble, "NPT" ) ) {
-+
-+
+    if (the_globals->haveTargetPressure()){
-+
+      bsInfo.targetPressure = the_globals->getTargetPressure();
-+
+      bsInfo.havePressure = 1;
-+
+    }
-+
+    else {
-+
+      sprintf( painCave.errMsg,
-+
+               "sysBuild error: If you use the constant pressure\n"
-+
+               "    ensemble, you must set targetPressure.\n"
-+
+               "    This was found in the BASS file.\n");
-+
+      painCave.isFatal = 1;
-+
+      simError();
-+
+    }
-+
-+
+    if (the_globals->haveTauThermostat()){
-+
+      bsInfo.tauThermostat = the_globals->getTauThermostat();
-+
+      bsInfo.haveTauThermostat = 1;;
-+
+    }
-+
+    else if (the_globals->haveQmass()){
-+
+      bsInfo.Qmass = the_globals->getQmass();
-+
+      bsInfo.haveQmass = 1;
-+
+    }
-+
+    else {
-+
+      sprintf( painCave.errMsg,
-+
+               "sysBuild error: If you use one of the constant temperature\n"
-+
+               "    ensembles, you must set either tauThermostat or qMass.\n"
-+
+               "    Neither of these was found in the BASS file.\n");
-+
+      painCave.isFatal = 1;
-+
+      simError();
-+
+    }
-+
-+
+    if (the_globals->haveTauBarostat()){
-+
+      bsInfo.tauBarostat = the_globals->getTauBarostat();
-+
+      bsInfo.haveTauBarostat = 1;
-+
+    }
-+
+    else {
-+
+      sprintf( painCave.errMsg,
-+
+               "sysBuild error: If you use the constant pressure\n"
-+
+               "    ensemble, you must set tauBarostat.\n"
-+
+               "    This was found in the BASS file.\n");
-+
+      painCave.isFatal = 1;
-+
+      simError();
-+
+    }
-+
-+
+  }
-+
+  else if ( !strcasecmp( bsInfo.ensemble, "NVT") ) {
-+
-+
+    if (the_globals->haveTauThermostat()){
-+
+      bsInfo.tauThermostat = the_globals->getTauThermostat();
-+
+      bsInfo.haveTauThermostat = 1;
-+
+    }
-+
+    else if (the_globals->haveQmass()){
-+
+      bsInfo.Qmass = the_globals->getQmass();
-+
+      bsInfo.haveQmass = 1;
-+
+    }
-+
+    else {
-+
+      sprintf( painCave.errMsg,
-+
+               "sysBuild error: If you use one of the constant temperature\n"
-+
+               "    ensembles, you must set either tauThermostat or qMass.\n"
-+
+               "    Neither of these was found in the BASS file.\n");
-+
+      painCave.isFatal = 1;
-+
+      simError();
-+
+    }
-+
-+
+  }
-+
+  else if ( !strcasecmp( bsInfo.ensemble, "NVE") ) {
-+
-+
+    // nothing special for now
-+
+  }
-+
+  else {
-+
+    sprintf( painCave.errMsg,
-+
+             "sysBuild Warning. Unrecognized Ensemble -> %s, "
-+
+             "reverting to NVE for this simulation.\n",
-+
+             bsInfo.ensemble );
-+
+    painCave.isFatal = 0;
-+
+    simError();
-+
+    strcpy( bsInfo.ensemble, "NVE" );
-+
+  }
-+
-+
-+
+  // get the components and calculate the tot_nMol and indvidual n_mol
-+
-+
+  the_components = the_globals->getComponents();
-+
+  bsInfo.componentsNmol = new int[bsInfo.nComponents];
-+
+  bsInfo.compStamps = new MoleculeStamp*[bsInfo.nComponents];
-+
+  bsInfo.totNmol = 0;
-+
+  for( i=0; i<bsInfo.nComponents; i++ ){
-+
-+
+    if( !the_components[i]->haveNMol() ){
-+
+      // we have a problem
-+
+      sprintf( painCave.errMsg,
-+
+               "sysBuild Error. No component NMol"
-+
+               " given. Cannot calculate the number of atoms.\n" );
-+
+      painCave.isFatal = 1;
-+
+      simError();
-+
+    }
-+
-+
+    bsInfo.totNmol += the_components[i]->getNMol();
-+
+    bsInfo.componentsNmol[i] = the_components[i]->getNMol();
-+
+  }
-+
-+
+  // make an array of molecule stamps that match the components used.
-+
+  // also extract the used stamps out into a separate linked list
-+
+  for( i=0; i<bsInfo.nComponents; i++ ){
-+
-+
+    id = the_components[i]->getType();
-+
+    bsInfo.compStamps[i] = NULL;
-+
-+
+    // check to make sure the component isn't already in the list
-+
-+
+    bsInfo.compStamps[i] = headStamp->match( id );
-+
+    if( bsInfo.compStamps[i] == NULL ){
-+
-+
+      // extract the component from the list;
-+
-+
+      currStamp = the_stamps->extractMolStamp( id );
-+
+      if( currStamp == NULL ){
-+
+        sprintf( painCave.errMsg,
-+
+                 "sysBuild error: Component \"%s\" was not found in the "
-+
+                 "list of declared molecules\n",
-+
+                 id );
-+
+        painCave.isFatal = 1;
-+
+        simError();
-+
+      }
-+
-+
+      headStamp->add( currStamp );
-+
+      bsInfo.compStamps[i] = headStamp->match( id );
-+
+    }
-+
+  }
-+
-+
+  // get and set the boxSize
-+
-+
+  if( the_globals->haveBox() ){
-+
+    bsInfo.boxX = the_globals->getBox();
-+
+    bsInfo.boxY = the_globals->getBox();
-+
+    bsInfo.boxZ = the_globals->getBox();
-+
+  }
-+
+  else if( the_globals->haveDensity() ){
-+
-+
+    double vol;
-+
+    vol = (double)bsInfo.totNmol / the_globals->getDensity();
-+
+    bsInfo.boxX = pow( vol, ( 1.0 / 3.0 ) );
-+
+    bsInfo.boxY = bsInfo.boxX;
-+
+    bsInfo.boxZ = bsInfo.boxY;
-+
+  }
-+
+  else{
-+
+    if( !the_globals->haveBoxX() ){
-+
+      sprintf( painCave.errMsg,
-+
+               "sysBuild error, no periodic BoxX size given.\n" );
-+
+      painCave.isFatal = 1;
-+
+      simError();
-+
+    }
-+
+    bsInfo.boxX = the_globals->getBoxX();
-+
-+
+    if( !the_globals->haveBoxY() ){
-+
+      sprintf( painCave.errMsg,
-+
+               "sysBuild error, no periodic BoxY size given.\n" );
-+
+      painCave.isFatal = 1;
-+
+      simError();
-+
+    }
-+
+    bsInfo.boxY = the_globals->getBoxY();
-+
-+
+    if( !the_globals->haveBoxZ() ){
-+
+      sprintf( painCave.errMsg,
-+
+               "SimSetup error, no periodic BoxZ size given.\n" );
-+
+      painCave.isFatal = 1;
-+
+      simError();
-+
+    }
-+
+    bsInfo.boxZ = the_globals->getBoxZ();
-+
+  }
-+
-+
+  //************************************************************
-+
+  // that should be all we need from bass. now to switch to the
-+
+  // appropriate system builder.
-+
+  // ***********************************************************
-+
-+
-+
+  switch( sysType ){
-+
-+
+  case BILAYER:
-+
-+
+    buildBilayer( isRandom );
-+
+    break;
-+
-+
+  case NANO:
-+
-+
-+
+    break;
-+
-+
+  default:
-+
+    sprintf( painCave.errMsg,
-+
+             "Unknown system type: %d\n", sysType );
-+
+    painCave.isFatal = 1;
-+
+    simError();
-+
-+
+  }
-+
-+
-+
+  // clean up memory;
-+
-+
+  if( headStamp!= NULL )       delete headStamp;
-+
+  if( the_stamps != NULL )     delete the_stamps;
-+
+  if( the_globals != NULL )    delete the_globals;
-+
+  if( the_components != NULL ) delete[] the_components;
-+
-+
+  if( bsInfo.componentsNmol != NULL ) delete[] bsInfo.componentsNmol;
-+
+  if( bsInfo.compStamps != NULL )     delete[] bsInfo.compStamps;
-+
+  if( bsInfo.includes != NULL ){
-+
+    prevInc = bsInfo.includes;
-+
+    while( prevInc != NULL ){
-+
+      currInc = prevInc->next;
-+
+      delete prevInc;
-+
+      prevInc = currInc;
-+
+    }
-+
+  }
-+
+  return 0;
+                "  ------\n"
+                "   -h              Display this message\n"
+                "   -o <prefix>     The output prefix\n"
-+
+                "   -I <include>    File name that should be included at the top of the\n"
-+
+                "                     output bass file.\n"
+                "   -r              toggle the random option\n"
+                "\n"
+                "  long:\n"
+                "  -----\n"
-<
+                "   --bilayer       Tries to build a basic bilayer with the specified number\n"
-<
+                "                     of lipids in the input bass file. The bilayer will be\n"
-<
+                "                     surrounded by the number of solvent molecules given\n"
-<
+                "                     in the bass file.\n"
-<
+                "                      -note: combined with \"-r\" the simulation will start in\n"
-<
+                "                             an FCC lattice with randomly assigned latice\n"
-<
+                "                             for all atoms involved.\n"
->
+                "   --bilayer <lipid> <water>  Tries to build a basic bilayer with the specified number\n"
->
+                "                              of lipids in the input bass file. The bilayer will be\n"
->
+                "                              surrounded by the number of solvent molecules given\n"
->
+                "                              in the bass file.\n"
->
+                "                                -note: combined with \"-r\" the simulation will start\n"
->
+                "                                 the lipids randomly oriented in a sea of waters.\n"
+                "\n"
+                "\n",
+                program_name);

Diff Legend

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

Comparing trunk/OOPSE/utils/sysBuild.cpp (file contents): Revision 495 by mmeineke, Mon Apr 14 19:52:00 2003 UTC vs. Revision 598 by chuckv, Mon Jul 14 21:35:45 2003 UTC

Diff Legend

Comparing trunk/OOPSE/utils/sysBuild.cpp (file contents):
Revision 495 by mmeineke, Mon Apr 14 19:52:00 2003 UTC vs.
Revision 598 by chuckv, Mon Jul 14 21:35:45 2003 UTC