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root/group/trunk/OOPSE/libmdtools/NPTi.cpp
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Comparing trunk/OOPSE/libmdtools/NPTi.cpp (file contents):
Revision 575 by gezelter, Tue Jul 8 21:06:14 2003 UTC vs.
Revision 855 by mmeineke, Thu Nov 6 22:01:37 2003 UTC

# Line 1 | Line 1
1 + #include <math.h>
2   #include "Atom.hpp"
3   #include "SRI.hpp"
4   #include "AbstractClasses.hpp"
# Line 6 | Line 7
7   #include "Thermo.hpp"
8   #include "ReadWrite.hpp"
9   #include "Integrator.hpp"
10 < #include "simError.h"
10 > #include "simError.h"
11  
12 + #ifdef IS_MPI
13 + #include "mpiSimulation.hpp"
14 + #endif
15  
16   // Basic isotropic thermostating and barostating via the Melchionna
17   // modification of the Hoover algorithm:
18   //
19   //    Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
20 < //       Molec. Phys., 78, 533.
20 > //       Molec. Phys., 78, 533.
21   //
22   //           and
23 < //
23 > //
24   //    Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
25  
26 < NPTi::NPTi ( SimInfo *theInfo, ForceFields* the_ff):
27 <  Integrator( theInfo, the_ff )
26 > template<typename T> NPTi<T>::NPTi ( SimInfo *theInfo, ForceFields* the_ff):
27 >  T( theInfo, the_ff )
28   {
29 <  chi = 0.0;
29 >  GenericData* data;
30 >  DoubleArrayData * etaValue;
31 >  vector<double> etaArray;
32 >
33    eta = 0.0;
34 <  have_tau_thermostat = 0;
35 <  have_tau_barostat = 0;
36 <  have_target_temp = 0;
37 <  have_target_pressure = 0;
34 >  oldEta = 0.0;
35 >
36 >  if( theInfo->useInitXSstate ){
37 >    // retrieve eta from simInfo if
38 >    data = info->getProperty(ETAVALUE_ID);
39 >    if(data){
40 >      etaValue = dynamic_cast<DoubleArrayData*>(data);
41 >      
42 >      if(etaValue){
43 >        etaArray = etaValue->getData();
44 >        eta = etaArray[0];
45 >        oldEta = eta;
46 >      }
47 >    }
48 >  }
49   }
50  
51 < void NPTi::moveA() {
52 <  
53 <  int i,j,k;
36 <  int atomIndex, aMatIndex;
37 <  DirectionalAtom* dAtom;
38 <  double Tb[3];
39 <  double ji[3];
40 <  double rj[3];
41 <  double instaTemp, instaPress, instaVol;
42 <  double tt2, tb2;
43 <  double angle;
51 > template<typename T> NPTi<T>::~NPTi() {
52 >  //nothing for now
53 > }
54  
55 <  tt2 = tauThermostat * tauThermostat;
56 <  tb2 = tauBarostat * tauBarostat;
55 > template<typename T> void NPTi<T>::resetIntegrator() {
56 >  eta = 0.0;
57 >  T::resetIntegrator();
58 > }
59  
60 <  instaTemp = tStats->getTemperature();
61 <  instaPress = tStats->getPressure();
62 <  instaVol = tStats->getVolume();
63 <  
64 <  // first evolve chi a half step
53 <  
54 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
55 <  eta += dt2 * ( instaVol * (instaPress - targetPressure) / (NkBT*tb2));
60 > template<typename T> void NPTi<T>::evolveEtaA() {
61 >  eta += dt2 * ( instaVol * (instaPress - targetPressure) /
62 >                 (p_convert*NkBT*tb2));
63 >  oldEta = eta;
64 > }
65  
66 <  for( i=0; i<nAtoms; i++ ){
58 <    atomIndex = i * 3;
59 <    aMatIndex = i * 9;
60 <    
61 <    // velocity half step
62 <    for( j=atomIndex; j<(atomIndex+3); j++ )
63 <      vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert
64 <                       - vel[j]*(chi+eta));
66 > template<typename T> void NPTi<T>::evolveEtaB() {
67  
68 <    // position whole step    
68 >  prevEta = eta;
69 >  eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) /
70 >                 (p_convert*NkBT*tb2));
71 > }
72  
73 <    for( j=atomIndex; j<(atomIndex+3); j=j+3 ) {
74 <      rj[0] = pos[j];
70 <      rj[1] = pos[j+1];
71 <      rj[2] = pos[j+2];
73 > template<typename T> void NPTi<T>::getVelScaleA(double sc[3], double vel[3]) {
74 >  int i;
75  
76 <      info->wrapVector(rj);
76 >  for(i=0; i<3; i++) sc[i] = vel[i] * ( chi + eta );
77 > }
78  
79 <      pos[j] += dt * (vel[j] + eta*rj[0]);
80 <      pos[j+1] += dt * (vel[j+1] + eta*rj[1]);
77 <      pos[j+2] += dt * (vel[j+2] + eta*rj[2]);
78 <    }
79 > template<typename T> void NPTi<T>::getVelScaleB(double sc[3], int index ){
80 >  int i;
81  
82 <    // Scale the box after all the positions have been moved:
82 >  for(i=0; i<3; i++) sc[i] = oldVel[index*3 + i] * ( chi + eta );
83 > }
84  
82 –    info->scaleBox(exp(dt*eta));
83 –  
84 –    if( atoms[i]->isDirectional() ){
85  
86 <      dAtom = (DirectionalAtom *)atoms[i];
87 <          
88 <      // get and convert the torque to body frame
89 <      
90 <      Tb[0] = dAtom->getTx();
91 <      Tb[1] = dAtom->getTy();
92 <      Tb[2] = dAtom->getTz();
93 <      
94 <      dAtom->lab2Body( Tb );
95 <      
96 <      // get the angular momentum, and propagate a half step
86 > template<typename T> void NPTi<T>::getPosScale(double pos[3], double COM[3],
87 >                                               int index, double sc[3]){
88 >  int j;
89  
90 <      ji[0] = dAtom->getJx();
91 <      ji[1] = dAtom->getJy();
92 <      ji[2] = dAtom->getJz();
93 <      
94 <      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi);
103 <      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi);
104 <      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi);
105 <      
106 <      // use the angular velocities to propagate the rotation matrix a
107 <      // full time step
108 <      
109 <      // rotate about the x-axis      
110 <      angle = dt2 * ji[0] / dAtom->getIxx();
111 <      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
112 <      
113 <      // rotate about the y-axis
114 <      angle = dt2 * ji[1] / dAtom->getIyy();
115 <      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
116 <      
117 <      // rotate about the z-axis
118 <      angle = dt * ji[2] / dAtom->getIzz();
119 <      this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] );
120 <      
121 <      // rotate about the y-axis
122 <      angle = dt2 * ji[1] / dAtom->getIyy();
123 <      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
124 <      
125 <       // rotate about the x-axis
126 <      angle = dt2 * ji[0] / dAtom->getIxx();
127 <      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
128 <      
129 <      dAtom->setJx( ji[0] );
130 <      dAtom->setJy( ji[1] );
131 <      dAtom->setJz( ji[2] );
132 <    }
133 <    
134 <  }
90 >  for(j=0; j<3; j++)
91 >    sc[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
92 >
93 >  for(j=0; j<3; j++)
94 >    sc[j] *= eta;
95   }
96  
97 < void NPTi::moveB( void ){
138 <  int i,j,k;
139 <  int atomIndex;
140 <  DirectionalAtom* dAtom;
141 <  double Tb[3];
142 <  double ji[3];
143 <  double instaTemp, instaPress, instaVol;
144 <  double tt2, tb2;
145 <  
146 <  tt2 = tauThermostat * tauThermostat;
147 <  tb2 = tauBarostat * tauBarostat;
97 > template<typename T> void NPTi<T>::scaleSimBox( void ){
98  
99 <  instaTemp = tStats->getTemperature();
150 <  instaPress = tStats->getPressure();
151 <  instaVol = tStats->getVolume();
99 >  double scaleFactor;
100  
101 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
154 <  eta += dt2 * ( instaVol * (instaPress - targetPressure) / (NkBT*tb2));
155 <  
156 <  for( i=0; i<nAtoms; i++ ){
157 <    atomIndex = i * 3;
158 <    
159 <    // velocity half step
160 <    for( j=atomIndex; j<(atomIndex+3); j++ )
161 <    for( j=atomIndex; j<(atomIndex+3); j++ )
162 <      vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert
163 <                       - vel[j]*(chi+eta));
164 <    
165 <    if( atoms[i]->isDirectional() ){
166 <      
167 <      dAtom = (DirectionalAtom *)atoms[i];
168 <      
169 <      // get and convert the torque to body frame
170 <      
171 <      Tb[0] = dAtom->getTx();
172 <      Tb[1] = dAtom->getTy();
173 <      Tb[2] = dAtom->getTz();
174 <      
175 <      dAtom->lab2Body( Tb );
176 <      
177 <      // get the angular momentum, and complete the angular momentum
178 <      // half step
179 <      
180 <      ji[0] = dAtom->getJx();
181 <      ji[1] = dAtom->getJy();
182 <      ji[2] = dAtom->getJz();
183 <      
184 <      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi);
185 <      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi);
186 <      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi);
187 <      
188 <      dAtom->setJx( ji[0] );
189 <      dAtom->setJy( ji[1] );
190 <      dAtom->setJz( ji[2] );
191 <    }
192 <  }
193 < }
101 >  scaleFactor = exp(dt*eta);
102  
103 < int NPTi::readyCheck() {
196 <
197 <  // First check to see if we have a target temperature.
198 <  // Not having one is fatal.
199 <  
200 <  if (!have_target_temp) {
103 >  if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) {
104      sprintf( painCave.errMsg,
105 <             "NPTi error: You can't use the NPTi integrator\n"
106 <             "   without a targetTemp!\n"
105 >             "NPTi error: Attempting a Box scaling of more than 10 percent"
106 >             " check your tauBarostat, as it is probably too small!\n"
107 >             " eta = %lf, scaleFactor = %lf\n", eta, scaleFactor
108               );
109      painCave.isFatal = 1;
110      simError();
111 <    return -1;
111 >  } else {
112 >    info->scaleBox(scaleFactor);
113    }
114  
115 <  if (!have_target_pressure) {
211 <    sprintf( painCave.errMsg,
212 <             "NPTi error: You can't use the NPTi integrator\n"
213 <             "   without a targetPressure!\n"
214 <             );
215 <    painCave.isFatal = 1;
216 <    simError();
217 <    return -1;
218 <  }
219 <  
220 <  // We must set tauThermostat.
221 <  
222 <  if (!have_tau_thermostat) {
223 <    sprintf( painCave.errMsg,
224 <             "NPTi error: If you use the NPTi\n"
225 <             "   integrator, you must set tauThermostat.\n");
226 <    painCave.isFatal = 1;
227 <    simError();
228 <    return -1;
229 <  }    
115 > }
116  
117 <  // We must set tauBarostat.
232 <  
233 <  if (!have_tau_barostat) {
234 <    sprintf( painCave.errMsg,
235 <             "NPTi error: If you use the NPTi\n"
236 <             "   integrator, you must set tauBarostat.\n");
237 <    painCave.isFatal = 1;
238 <    simError();
239 <    return -1;
240 <  }    
117 > template<typename T> bool NPTi<T>::etaConverged() {
118  
119 <  // We need NkBT a lot, so just set it here:
119 >  return ( fabs(prevEta - eta) <= etaTolerance );
120 > }
121  
122 <  NkBT = (double)info->ndf * kB * targetTemp;
122 > template<typename T> double NPTi<T>::getConservedQuantity(void){
123  
124 <  return 1;
124 >  double conservedQuantity;
125 >  double Energy;
126 >  double thermostat_kinetic;
127 >  double thermostat_potential;
128 >  double barostat_kinetic;
129 >  double barostat_potential;
130 >
131 >  Energy = tStats->getTotalE();
132 >
133 >  thermostat_kinetic = fkBT* tt2 * chi * chi /
134 >    (2.0 * eConvert);
135 >
136 >  thermostat_potential = fkBT* integralOfChidt / eConvert;
137 >
138 >
139 >  barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta /
140 >    (2.0 * eConvert);
141 >
142 >  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
143 >    eConvert;
144 >
145 >  conservedQuantity = Energy + thermostat_kinetic + thermostat_potential +
146 >    barostat_kinetic + barostat_potential;
147 >
148 > //   cout.width(8);
149 > //   cout.precision(8);
150 >
151 > //   cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
152 > //       "\t" << thermostat_potential << "\t" << barostat_kinetic <<
153 > //       "\t" << barostat_potential << "\t" << conservedQuantity << endl;
154 >  return conservedQuantity;
155   }
156 +
157 + template<typename T> string NPTi<T>::getAdditionalParameters(void){
158 +  string parameters;
159 +  const int BUFFERSIZE = 2000; // size of the read buffer
160 +  char buffer[BUFFERSIZE];
161 +
162 +  sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
163 +  parameters += buffer;
164 +
165 +  sprintf(buffer,"\t%G\t0\t0;", eta);
166 +  parameters += buffer;
167 +
168 +  sprintf(buffer,"\t0\t%G\t0;", eta);
169 +  parameters += buffer;
170 +
171 +  sprintf(buffer,"\t0\t0\t%G;", eta);
172 +  parameters += buffer;
173 +
174 +  return parameters;
175 +
176 + }

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