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root/group/trunk/OOPSE/libmdtools/NPTi.cpp
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Comparing trunk/OOPSE/libmdtools/NPTi.cpp (file contents):
Revision 577 by gezelter, Wed Jul 9 01:41:11 2003 UTC vs.
Revision 853 by mmeineke, Thu Nov 6 19:11:38 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;
28 <  have_tau_barostat = 0;
29 <  have_target_temp = 0;
30 <  have_target_pressure = 0;
31 < }
34 >  oldEta = 0.0;
35  
36 < void NPTi::moveA() {
37 <  
38 <  int i,j,k;
39 <  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;
36 >  // retrieve eta from simInfo if
37 >  data = info->getProperty(ETAVALUE_ID);
38 >  if(data){
39 >    etaValue = dynamic_cast<DoubleArrayData*>(data);
40  
41 <  tt2 = tauThermostat * tauThermostat;
42 <  tb2 = tauBarostat * tauBarostat;
41 >    if(etaValue){
42 >      etaArray = etaValue->getData();
43 >      eta = etaArray[0];
44 >      oldEta = eta;
45 >    }
46 >  }
47  
48 <  instaTemp = tStats->getTemperature();
49 <  instaPress = tStats->getPressure();
50 <  instaVol = tStats->getVolume();
51 <  
52 <  // first evolve chi a half step
53 <  
54 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
55 <  eta += dt2 * ( instaVol * (instaPress - targetPressure) / (NkBT*tb2));
48 > }
49  
50 <  for( i=0; i<nAtoms; i++ ){
51 <    atomIndex = i * 3;
52 <    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));
50 > template<typename T> NPTi<T>::~NPTi() {
51 >  //nothing for now
52 > }
53  
54 <    // position whole step    
54 > template<typename T> void NPTi<T>::resetIntegrator() {
55 >  eta = 0.0;
56 >  T::resetIntegrator();
57 > }
58  
59 <    rj[0] = pos[atomIndex];
60 <    rj[1] = pos[atomIndex+1];
61 <    rj[2] = pos[atomIndex+2];
62 <    
63 <    info->wrapVector(rj);
59 > template<typename T> void NPTi<T>::evolveEtaA() {
60 >  eta += dt2 * ( instaVol * (instaPress - targetPressure) /
61 >                 (p_convert*NkBT*tb2));
62 >  oldEta = eta;
63 > }
64  
65 <    pos[atomIndex] += dt * (vel[atomIndex] + eta*rj[0]);
75 <    pos[atomIndex+1] += dt * (vel[atomIndex+1] + eta*rj[1]);
76 <    pos[atomIndex+2] += dt * (vel[atomIndex+2] + eta*rj[2]);
77 <  
78 <    if( atoms[i]->isDirectional() ){
65 > template<typename T> void NPTi<T>::evolveEtaB() {
66  
67 <      dAtom = (DirectionalAtom *)atoms[i];
68 <          
69 <      // get and convert the torque to body frame
70 <      
84 <      Tb[0] = dAtom->getTx();
85 <      Tb[1] = dAtom->getTy();
86 <      Tb[2] = dAtom->getTz();
87 <      
88 <      dAtom->lab2Body( Tb );
89 <      
90 <      // get the angular momentum, and propagate a half step
67 >  prevEta = eta;
68 >  eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) /
69 >                 (p_convert*NkBT*tb2));
70 > }
71  
72 <      ji[0] = dAtom->getJx();
73 <      ji[1] = dAtom->getJy();
94 <      ji[2] = dAtom->getJz();
95 <      
96 <      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi);
97 <      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi);
98 <      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi);
99 <      
100 <      // use the angular velocities to propagate the rotation matrix a
101 <      // full time step
102 <      
103 <      // rotate about the x-axis      
104 <      angle = dt2 * ji[0] / dAtom->getIxx();
105 <      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
106 <      
107 <      // rotate about the y-axis
108 <      angle = dt2 * ji[1] / dAtom->getIyy();
109 <      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
110 <      
111 <      // rotate about the z-axis
112 <      angle = dt * ji[2] / dAtom->getIzz();
113 <      this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] );
114 <      
115 <      // rotate about the y-axis
116 <      angle = dt2 * ji[1] / dAtom->getIyy();
117 <      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
118 <      
119 <       // rotate about the x-axis
120 <      angle = dt2 * ji[0] / dAtom->getIxx();
121 <      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
122 <      
123 <      dAtom->setJx( ji[0] );
124 <      dAtom->setJy( ji[1] );
125 <      dAtom->setJz( ji[2] );
126 <    }
127 <    
128 <  }
129 <  // Scale the box after all the positions have been moved:
72 > template<typename T> void NPTi<T>::getVelScaleA(double sc[3], double vel[3]) {
73 >  int i;
74  
75 <  info->scaleBox(exp(dt*eta));
75 >  for(i=0; i<3; i++) sc[i] = vel[i] * ( chi + eta );
76 > }
77  
78 + template<typename T> void NPTi<T>::getVelScaleB(double sc[3], int index ){
79 +  int i;
80 +
81 +  for(i=0; i<3; i++) sc[i] = oldVel[index*3 + i] * ( chi + eta );
82   }
83  
135 – void NPTi::moveB( void ){
136 –  int i,j,k;
137 –  int atomIndex;
138 –  DirectionalAtom* dAtom;
139 –  double Tb[3];
140 –  double ji[3];
141 –  double instaTemp, instaPress, instaVol;
142 –  double tt2, tb2;
143 –  
144 –  tt2 = tauThermostat * tauThermostat;
145 –  tb2 = tauBarostat * tauBarostat;
84  
85 <  instaTemp = tStats->getTemperature();
86 <  instaPress = tStats->getPressure();
87 <  instaVol = tStats->getVolume();
85 > template<typename T> void NPTi<T>::getPosScale(double pos[3], double COM[3],
86 >                                               int index, double sc[3]){
87 >  int j;
88  
89 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
90 <  eta += dt2 * ( instaVol * (instaPress - targetPressure) / (NkBT*tb2));
91 <  
92 <  for( i=0; i<nAtoms; i++ ){
93 <    atomIndex = i * 3;
156 <    
157 <    // velocity half step
158 <    for( j=atomIndex; j<(atomIndex+3); j++ )
159 <    for( j=atomIndex; j<(atomIndex+3); j++ )
160 <      vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert
161 <                       - vel[j]*(chi+eta));
162 <    
163 <    if( atoms[i]->isDirectional() ){
164 <      
165 <      dAtom = (DirectionalAtom *)atoms[i];
166 <      
167 <      // get and convert the torque to body frame
168 <      
169 <      Tb[0] = dAtom->getTx();
170 <      Tb[1] = dAtom->getTy();
171 <      Tb[2] = dAtom->getTz();
172 <      
173 <      dAtom->lab2Body( Tb );
174 <      
175 <      // get the angular momentum, and complete the angular momentum
176 <      // half step
177 <      
178 <      ji[0] = dAtom->getJx();
179 <      ji[1] = dAtom->getJy();
180 <      ji[2] = dAtom->getJz();
181 <      
182 <      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi);
183 <      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi);
184 <      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi);
185 <      
186 <      dAtom->setJx( ji[0] );
187 <      dAtom->setJy( ji[1] );
188 <      dAtom->setJz( ji[2] );
189 <    }
190 <  }
89 >  for(j=0; j<3; j++)
90 >    sc[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
91 >
92 >  for(j=0; j<3; j++)
93 >    sc[j] *= eta;
94   }
95  
96 < int NPTi::readyCheck() {
194 <
195 <  // First check to see if we have a target temperature.
196 <  // Not having one is fatal.
197 <  
198 <  if (!have_target_temp) {
199 <    sprintf( painCave.errMsg,
200 <             "NPTi error: You can't use the NPTi integrator\n"
201 <             "   without a targetTemp!\n"
202 <             );
203 <    painCave.isFatal = 1;
204 <    simError();
205 <    return -1;
206 <  }
96 > template<typename T> void NPTi<T>::scaleSimBox( void ){
97  
98 <  if (!have_target_pressure) {
98 >  double scaleFactor;
99 >
100 >  scaleFactor = exp(dt*eta);
101 >
102 >  if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) {
103      sprintf( painCave.errMsg,
104 <             "NPTi error: You can't use the NPTi integrator\n"
105 <             "   without a targetPressure!\n"
104 >             "NPTi error: Attempting a Box scaling of more than 10 percent"
105 >             " check your tauBarostat, as it is probably too small!\n"
106 >             " eta = %lf, scaleFactor = %lf\n", eta, scaleFactor
107               );
108      painCave.isFatal = 1;
109      simError();
110 <    return -1;
110 >  } else {
111 >    info->scaleBox(scaleFactor);
112    }
217 –  
218 –  // We must set tauThermostat.
219 –  
220 –  if (!have_tau_thermostat) {
221 –    sprintf( painCave.errMsg,
222 –             "NPTi error: If you use the NPTi\n"
223 –             "   integrator, you must set tauThermostat.\n");
224 –    painCave.isFatal = 1;
225 –    simError();
226 –    return -1;
227 –  }    
113  
114 <  // We must set tauBarostat.
230 <  
231 <  if (!have_tau_barostat) {
232 <    sprintf( painCave.errMsg,
233 <             "NPTi error: If you use the NPTi\n"
234 <             "   integrator, you must set tauBarostat.\n");
235 <    painCave.isFatal = 1;
236 <    simError();
237 <    return -1;
238 <  }    
114 > }
115  
116 <  // We need NkBT a lot, so just set it here:
116 > template<typename T> bool NPTi<T>::etaConverged() {
117  
118 <  NkBT = (double)info->ndf * kB * targetTemp;
118 >  return ( fabs(prevEta - eta) <= etaTolerance );
119 > }
120  
121 <  return 1;
121 > template<typename T> double NPTi<T>::getConservedQuantity(void){
122 >
123 >  double conservedQuantity;
124 >  double Energy;
125 >  double thermostat_kinetic;
126 >  double thermostat_potential;
127 >  double barostat_kinetic;
128 >  double barostat_potential;
129 >
130 >  Energy = tStats->getTotalE();
131 >
132 >  thermostat_kinetic = fkBT* tt2 * chi * chi /
133 >    (2.0 * eConvert);
134 >
135 >  thermostat_potential = fkBT* integralOfChidt / eConvert;
136 >
137 >
138 >  barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta /
139 >    (2.0 * eConvert);
140 >
141 >  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
142 >    eConvert;
143 >
144 >  conservedQuantity = Energy + thermostat_kinetic + thermostat_potential +
145 >    barostat_kinetic + barostat_potential;
146 >
147 > //   cout.width(8);
148 > //   cout.precision(8);
149 >
150 > //   cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
151 > //       "\t" << thermostat_potential << "\t" << barostat_kinetic <<
152 > //       "\t" << barostat_potential << "\t" << conservedQuantity << endl;
153 >  return conservedQuantity;
154   }
155 +
156 + template<typename T> string NPTi<T>::getAdditionalParameters(void){
157 +  string parameters;
158 +  const int BUFFERSIZE = 2000; // size of the read buffer
159 +  char buffer[BUFFERSIZE];
160 +
161 +  sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
162 +  parameters += buffer;
163 +
164 +  sprintf(buffer,"\t%G\t0\t0;", eta);
165 +  parameters += buffer;
166 +
167 +  sprintf(buffer,"\t0\t%G\t0;", eta);
168 +  parameters += buffer;
169 +
170 +  sprintf(buffer,"\t0\t0\t%G;", eta);
171 +  parameters += buffer;
172 +
173 +  return parameters;
174 +
175 + }

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