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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 1287 by gezelter, Wed Sep 10 18:11:32 2008 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 6 | Line 6
6   * redistribute this software in source and binary code form, provided
7   * that the following conditions are met:
8   *
9 < * 1. Acknowledgement of the program authors must be made in any
10 < *    publication of scientific results based in part on use of the
11 < *    program.  An acceptable form of acknowledgement is citation of
12 < *    the article in which the program was described (Matthew
13 < *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 < *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 < *    Parallel Simulation Engine for Molecular Dynamics,"
16 < *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 < *
18 < * 2. Redistributions of source code must retain the above copyright
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
12 > * 2. Redistributions in binary form must reproduce the above copyright
13   *    notice, this list of conditions and the following disclaimer in the
14   *    documentation and/or other materials provided with the
15   *    distribution.
# Line 37 | Line 28
28   * arising out of the use of or inability to use software, even if the
29   * University of Notre Dame has been advised of the possibility of
30   * such damages.
31 + *
32 + * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33 + * research, please cite the appropriate papers when you publish your
34 + * work.  Good starting points are:
35 + *                                                                      
36 + * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37 + * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 + * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 + * [4]  Vardeman & Gezelter, in progress (2009).                        
40   */
41  
42   /**
# Line 74 | Line 74
74   #include "UseTheForce/DarkSide/simParallel_interface.h"
75   #endif
76  
77 < namespace oopse {
77 > namespace OpenMD {
78    std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
79      std::map<int, std::set<int> >::iterator i = container.find(index);
80      std::set<int> result;
# Line 446 | Line 446 | namespace oopse {
446        b = torsion->getAtomB()->getGlobalIndex();        
447        c = torsion->getAtomC()->getGlobalIndex();        
448        d = torsion->getAtomD()->getGlobalIndex();      
449 <  
449 >
450        if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
451          oneTwoInteractions_.addPair(a, b);      
452          oneTwoInteractions_.addPair(b, c);
# Line 763 | Line 763 | namespace oopse {
763      useRF = 0;
764      useSF = 0;
765      useSP = 0;
766 +    useBoxDipole = 0;
767  
768  
769      if (simParams_->haveElectrostaticSummationMethod()) {
# Line 950 | Line 951 | namespace oopse {
951      nOneThree = oneThreeInteractions_.getSize();
952      nOneFour = oneFourInteractions_.getSize();
953  
953 –    std::cerr << "exculdes:\n";
954 –    std::cerr << excludedInteractions_;
955 –    std::cerr << "\noneTwo:\n";
956 –    std::cerr << oneTwoInteractions_;
957 –    std::cerr << "\noneThree:\n";
958 –    std::cerr << oneThreeInteractions_;
959 –    std::cerr << "\noneFour:\n";
960 –    std::cerr << oneFourInteractions_;
961 –
954      int* excludeList = excludedInteractions_.getPairList();
955      int* oneTwoList = oneTwoInteractions_.getPairList();
956      int* oneThreeList = oneThreeInteractions_.getPairList();
# Line 977 | Line 969 | namespace oopse {
969        sprintf( painCave.errMsg,
970                 "There was an error setting the simulation information in fortran.\n" );
971        painCave.isFatal = 1;
972 <      painCave.severity = OOPSE_ERROR;
972 >      painCave.severity = OPENMD_ERROR;
973        simError();
974      }
975      
# Line 1061 | Line 1053 | namespace oopse {
1053      int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1054  
1055      // Set LJ shifting bools to false
1056 <    ljsp_ = false;
1057 <    ljsf_ = false;
1056 >    ljsp_ = 0;
1057 >    ljsf_ = 0;
1058  
1059      std::string myPolicy;
1060      if (forceFieldOptions_.haveCutoffPolicy()){
# Line 1113 | Line 1105 | namespace oopse {
1105            rsw_ = 0.85 * rcut_;
1106            sprintf(painCave.errMsg,
1107                    "SimCreator Warning: No value was set for the switchingRadius.\n"
1108 <                  "\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1108 >                  "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
1109                    "\tswitchingRadius = %f. for this simulation\n", rsw_);
1110          painCave.isFatal = 0;
1111          simError();
# Line 1121 | Line 1113 | namespace oopse {
1113            rsw_ = rcut_;
1114            sprintf(painCave.errMsg,
1115                    "SimCreator Warning: No value was set for the switchingRadius.\n"
1116 <                  "\tOOPSE will use the same value as the cutoffRadius.\n"
1116 >                  "\tOpenMD will use the same value as the cutoffRadius.\n"
1117                    "\tswitchingRadius = %f. for this simulation\n", rsw_);
1118            painCave.isFatal = 0;
1119            simError();
# Line 1133 | Line 1125 | namespace oopse {
1125          toUpper(myMethod);
1126          
1127          if (myMethod == "SHIFTED_POTENTIAL") {
1128 <          ljsp_ = true;
1128 >          ljsp_ = 1;
1129          } else if (myMethod == "SHIFTED_FORCE") {
1130 <          ljsf_ = true;
1130 >          ljsf_ = 1;
1131          }
1132        }
1133 +
1134        notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1135        
1136      } else {
# Line 1146 | Line 1139 | namespace oopse {
1139        if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1140          sprintf(painCave.errMsg,
1141                  "SimCreator Warning: No value was set for the cutoffRadius.\n"
1142 <                "\tOOPSE will use a default value of 15.0 angstroms"
1142 >                "\tOpenMD will use a default value of 15.0 angstroms"
1143                  "\tfor the cutoffRadius.\n");
1144          painCave.isFatal = 0;
1145          simError();
# Line 1159 | Line 1152 | namespace oopse {
1152        // For the time being, we're tethering the LJ shifted behavior to the
1153        // electrostaticSummationMethod keyword options
1154            if (myMethod == "SHIFTED_POTENTIAL") {
1155 <            ljsp_ = true;
1155 >            ljsp_ = 1;
1156            } else if (myMethod == "SHIFTED_FORCE") {
1157 <            ljsf_ = true;
1157 >            ljsf_ = 1;
1158            }
1159            if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1160              if (simParams_->haveSwitchingRadius()){
# Line 1180 | Line 1173 | namespace oopse {
1173          } else {        
1174            sprintf(painCave.errMsg,
1175                    "SimCreator Warning: No value was set for switchingRadius.\n"
1176 <                  "\tOOPSE will use a default value of\n"
1176 >                  "\tOpenMD will use a default value of\n"
1177                    "\t0.85 * cutoffRadius for the switchingRadius\n");
1178            painCave.isFatal = 0;
1179            simError();
# Line 1641 | Line 1634 | namespace oopse {
1634        return sdByGlobalIndex_.at(index);
1635      }  
1636   */  
1637 < }//end namespace oopse
1637 > }//end namespace OpenMD
1638  

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