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Comparing trunk/src/restraints/ThermoIntegrationForceManager.cpp (file contents):
Revision 665 by tim, Thu Oct 13 22:26:47 2005 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 < #include <cmath>
42 >
43   #include "restraints/ThermoIntegrationForceManager.hpp"
44 – #include "integrators/Integrator.hpp"
45 – #include "math/SquareMatrix3.hpp"
46 – #include "primitives/Molecule.hpp"
47 – #include "utils/simError.h"
48 – #include "utils/OOPSEConstant.hpp"
49 – #include "utils/StringUtils.hpp"
44  
45 < namespace oopse {
45 > #ifdef IS_MPI
46 > #include <mpi.h>
47 > #endif
48 >
49 > namespace OpenMD {
50    
51    ThermoIntegrationForceManager::ThermoIntegrationForceManager(SimInfo* info):
52 <    ForceManager(info){
53 <      currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
54 <      simParam = info_->getSimParams();
52 >    RestraintForceManager(info){
53 >    currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
54 >    simParam = info_->getSimParams();
55      
56 <      if (simParam->haveThermodynamicIntegrationLambda()){
57 <        tIntLambda_ = simParam->getThermodynamicIntegrationLambda();
58 <      }
59 <      else{
60 <        tIntLambda_ = 1.0;
61 <        sprintf(painCave.errMsg,
62 <                "ThermoIntegration error: the transformation parameter (lambda) was\n"
63 <                "\tnot specified. OOPSE will use a default value of %f. To set\n"
64 <                "\tlambda, use the thermodynamicIntegrationLambda variable.\n",
65 <                tIntLambda_);
66 <        painCave.isFatal = 0;
67 <        simError();
68 <      }
56 >    if (simParam->haveThermodynamicIntegrationLambda()){
57 >      tIntLambda_ = simParam->getThermodynamicIntegrationLambda();
58 >    }
59 >    else{
60 >      tIntLambda_ = 1.0;
61 >      sprintf(painCave.errMsg,
62 >              "ThermoIntegration error: the transformation parameter\n"
63 >              "\t(lambda) was not specified. OpenMD will use a default\n"
64 >              "\tvalue of %f. To set lambda, use the \n"
65 >              "\tthermodynamicIntegrationLambda variable.\n",
66 >              tIntLambda_);
67 >      painCave.isFatal = 0;
68 >      simError();
69 >    }
70      
71 <      if (simParam->haveThermodynamicIntegrationK()){
72 <        tIntK_ = simParam->getThermodynamicIntegrationK();
74 <      }
75 <      else{
76 <        tIntK_ = 1.0;
77 <        sprintf(painCave.errMsg,
78 <                "ThermoIntegration Warning: the tranformation parameter exponent\n"
79 <                "\t(k) was not specified. OOPSE will use a default value of %f.\n"
80 <                "\tTo set k, use the thermodynamicIntegrationK variable.\n",
81 <                tIntK_);
82 <        painCave.isFatal = 0;
83 <        simError();      
84 <      }
85 <    
86 <      if (simParam->getUseSolidThermInt()) {
87 <        // build a restraint object
88 <        restraint_ =  new Restraints(info_, tIntLambda_, tIntK_);
89 <      
90 <      }
91 <    
92 <      // build the scaling factor used to modulate the forces and torques
93 <      factor_ = pow(tIntLambda_, tIntK_);
94 <
71 >    if (simParam->haveThermodynamicIntegrationK()){
72 >      tIntK_ = simParam->getThermodynamicIntegrationK();
73      }
74 +    else{
75 +      tIntK_ = 1.0;
76 +      sprintf(painCave.errMsg,
77 +              "ThermoIntegration Warning: the tranformation parameter\n"
78 +              "\texponent (k) was not specified. OpenMD will use a default\n"
79 +              "\tvalue of %f. To set k, use the thermodynamicIntegrationK\n"
80 +              "\tvariable.\n",
81 +              tIntK_);
82 +      painCave.isFatal = 0;
83 +      simError();      
84 +    }
85 +    
86 +    // build the scaling factor used to modulate the forces and torques
87 +    factor_ = pow(tIntLambda_, tIntK_);
88 +  }
89    
90    ThermoIntegrationForceManager::~ThermoIntegrationForceManager(){
91    }
# Line 131 | Line 124 | namespace oopse {
124          }
125        }
126      }
127 <  
127 >    
128      // set vraw to be the unmodulated potential
129      lrPot_ = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
130      curSnapshot->statData[Stats::VRAW] = lrPot_;
# Line 145 | Line 138 | namespace oopse {
138      tempTau *= factor_;
139      curSnapshot->statData.setTau(tempTau);
140  
141 <    // do crystal restraint forces for thermodynamic integration
142 <    if (simParam->getUseSolidThermInt()) {
143 <      
151 <      lrPot_ += restraint_->Calc_Restraint_Forces();
152 <      curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot_;
153 <      
154 <      vHarm_ = restraint_->getVharm();
155 <      curSnapshot->statData[Stats::VHARM] = vHarm_;
156 <    }
141 >    // now, on to the applied restraining potentials (if needed):
142 >    RealType restPot_local = 0.0;
143 >    RealType vHarm_local = 0.0;
144      
145 <  }
146 <  
145 >    if (simParam->getUseRestraints()) {
146 >      // do restraints from RestraintForceManager:
147 >      //restPot_local = doRestraints(1.0 - factor_);    
148 >      restPot_local = doRestraints(1.0 - factor_);      
149 >      vHarm_local = getUnscaledPotential();
150 >    }
151 >      
152 > #ifdef IS_MPI
153 >    RealType restPot;
154 >    MPI::COMM_WORLD.Allreduce(&restPot_local, &restPot, 1,
155 >                              MPI::REALTYPE, MPI::SUM);
156 >    MPI::COMM_WORLD.Allreduce(&vHarm_local, &vHarm_, 1,
157 >                              MPI::REALTYPE, MPI::SUM);        
158 >    lrPot_ += restPot;
159 > #else
160 >    lrPot_ += restPot_local;
161 >    vHarm_ = vHarm_local;
162 > #endif
163 >
164 >    // give the final values to stats
165 >    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot_;
166 >    curSnapshot->statData[Stats::VHARM] = vHarm_;
167 >  }  
168   }

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