OOPSE/libmdtools/NPTi.cpp

#include <cmath>
#include "Atom.hpp"
#include "SRI.hpp"
#include "AbstractClasses.hpp"
#include "SimInfo.hpp"
#include "ForceFields.hpp"
#include "Thermo.hpp"
#include "ReadWrite.hpp"
#include "Integrator.hpp"
#include "simError.h" 


// Basic isotropic thermostating and barostating via the Melchionna
// modification of the Hoover algorithm:
//
//    Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
//       Molec. Phys., 78, 533. 
//
//           and
// 
//    Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.

NPTi::NPTi ( SimInfo *theInfo, ForceFields* the_ff):
  Integrator( theInfo, the_ff )
{
  chi = 0.0;
  eta = 0.0;
  have_tau_thermostat = 0;
  have_tau_barostat = 0;
  have_target_temp = 0;
  have_target_pressure = 0;
}

void NPTi::moveA() {
  
  int i, j;
  DirectionalAtom* dAtom;
  double Tb[3], ji[3];
  double A[3][3], I[3][3];
  double angle, mass;
  double vel[3], pos[3], frc[3];

  double rj[3];
  double instaTemp, instaPress, instaVol;
  double tt2, tb2;

  tt2 = tauThermostat * tauThermostat;
  tb2 = tauBarostat * tauBarostat;

  instaTemp = tStats->getTemperature();
  instaPress = tStats->getPressure();
  instaVol = tStats->getVolume();
   
   // first evolve chi a half step
  
  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
  eta += dt2 * ( instaVol * (instaPress - targetPressure) / 
                 (p_convert*NkBT*tb2));

  for( i=0; i<nAtoms; i++ ){
    atoms[i]->getVel( vel );
    atoms[i]->getPos( pos );
    atoms[i]->getFrc( frc );

    mass = atoms[i]->getMass();

    for (j=0; j < 3; j++) {
      vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi+eta));
      rj[j] = pos[j];
    }

    atoms[i]->setVel( vel );

    info->wrapVector(rj);

    for (j = 0; j < 3; j++) 
      pos[j] += dt * (vel[j] + eta*rj[j]);


    atoms[i]->setPos( pos );


    if( atoms[i]->isDirectional() ){

      dAtom = (DirectionalAtom *)atoms[i];
          
      // get and convert the torque to body frame
      
      dAtom->getTrq( Tb );
      dAtom->lab2Body( Tb );
      
      // get the angular momentum, and propagate a half step

      dAtom->getJ( ji );

      for (j=0; j < 3; j++) 
        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
      
      // use the angular velocities to propagate the rotation matrix a
      // full time step

      dAtom->getA(A);
      dAtom->getI(I);
    
      // rotate about the x-axis      
      angle = dt2 * ji[0] / I[0][0];
      this->rotate( 1, 2, angle, ji, A ); 

      // rotate about the y-axis
      angle = dt2 * ji[1] / I[1][1];
      this->rotate( 2, 0, angle, ji, A );
      
      // rotate about the z-axis
      angle = dt * ji[2] / I[2][2];
      this->rotate( 0, 1, angle, ji, A);
      
      // rotate about the y-axis
      angle = dt2 * ji[1] / I[1][1];
      this->rotate( 2, 0, angle, ji, A );
      
       // rotate about the x-axis
      angle = dt2 * ji[0] / I[0][0];
      this->rotate( 1, 2, angle, ji, A );
      
      dAtom->setJ( ji );
      dAtom->setA( A  );    
    }                

  }
  // Scale the box after all the positions have been moved:
  
  cerr << "eta = " << eta 
       << "; exp(dt*eta) = " << exp(eta*dt) << "\n";
  
  info->scaleBox(exp(dt*eta));  
}

void NPTi::moveB( void ){

  int i, j;
  DirectionalAtom* dAtom;
  double Tb[3], ji[3];
  double vel[3], frc[3];
  double mass;

  double instaTemp, instaPress, instaVol;
  double tt2, tb2;
  
  tt2 = tauThermostat * tauThermostat;
  tb2 = tauBarostat * tauBarostat;

  instaTemp = tStats->getTemperature();
  instaPress = tStats->getPressure();
  instaVol = tStats->getVolume();

  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
  eta += dt2 * ( instaVol * (instaPress - targetPressure) / 
                 (p_convert*NkBT*tb2));
  
  for( i=0; i<nAtoms; i++ ){

    atoms[i]->getVel( vel );
    atoms[i]->getFrc( frc );

    mass = atoms[i]->getMass();

    // velocity half step
    for (j=0; j < 3; j++) 
      vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi+eta));
    
    atoms[i]->setVel( vel );

    if( atoms[i]->isDirectional() ){

      dAtom = (DirectionalAtom *)atoms[i];

      // get and convert the torque to body frame      

      dAtom->getTrq( Tb );
      dAtom->lab2Body( Tb );

      // get the angular momentum, and propagate a half step

      dAtom->getJ( ji );

      for (j=0; j < 3; j++) 
        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);     

      dAtom->setJ( ji );
    }
  }
}

int NPTi::readyCheck() {
 
  // First check to see if we have a target temperature. 
  // Not having one is fatal. 
  
  if (!have_target_temp) {
    sprintf( painCave.errMsg,
             "NPTi error: You can't use the NPTi integrator\n"
             "   without a targetTemp!\n"
             );
    painCave.isFatal = 1;
    simError();
    return -1;
  }

  if (!have_target_pressure) {
    sprintf( painCave.errMsg,
             "NPTi error: You can't use the NPTi integrator\n"
             "   without a targetPressure!\n"
             );
    painCave.isFatal = 1;
    simError();
    return -1;
  }
  
  // We must set tauThermostat.
   
  if (!have_tau_thermostat) {
    sprintf( painCave.errMsg,
             "NPTi error: If you use the NPTi\n"
             "   integrator, you must set tauThermostat.\n");
    painCave.isFatal = 1;
    simError();
    return -1;
  }    

  // We must set tauBarostat.
   
  if (!have_tau_barostat) {
    sprintf( painCave.errMsg,
             "NPTi error: If you use the NPTi\n"
             "   integrator, you must set tauBarostat.\n");
    painCave.isFatal = 1;
    simError();
    return -1;
  }    

  // We need NkBT a lot, so just set it here:

  NkBT = (double)info->ndf * kB * targetTemp;

  return 1;
}
Revision:	600
Committed:	Mon Jul 14 22:38:13 2003 UTC (20 years, 11 months ago) by gezelter
File size:	5658 byte(s)
Log Message:	Fixes for get and set routines in Atom and DirectionalAtom
#	User	Rev	Content
1	gezelter	578	#include <cmath>
2	gezelter	574	#include "Atom.hpp"
3			#include "SRI.hpp"
4			#include "AbstractClasses.hpp"
5			#include "SimInfo.hpp"
6			#include "ForceFields.hpp"
7			#include "Thermo.hpp"
8			#include "ReadWrite.hpp"
9			#include "Integrator.hpp"
10			#include "simError.h"
11
12
13			// Basic isotropic thermostating and barostating via the Melchionna
14			// modification of the Hoover algorithm:
15			//
16			// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
17			// Molec. Phys., 78, 533.
18			//
19			// and
20			//
21			// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
22
23			NPTi::NPTi ( SimInfo theInfo, ForceFields the_ff):
24			Integrator( theInfo, the_ff )
25			{
26			chi = 0.0;
27			eta = 0.0;
28			have_tau_thermostat = 0;
29			have_tau_barostat = 0;
30			have_target_temp = 0;
31			have_target_pressure = 0;
32			}
33
34			void NPTi::moveA() {
35
36	gezelter	600	int i, j;
37	gezelter	574	DirectionalAtom* dAtom;
38	gezelter	600	double Tb[3], ji[3];
39			double A[3][3], I[3][3];
40			double angle, mass;
41			double vel[3], pos[3], frc[3];
42
43	gezelter	574	double rj[3];
44			double instaTemp, instaPress, instaVol;
45			double tt2, tb2;
46
47			tt2 = tauThermostat * tauThermostat;
48			tb2 = tauBarostat * tauBarostat;
49
50			instaTemp = tStats->getTemperature();
51			instaPress = tStats->getPressure();
52			instaVol = tStats->getVolume();
53
54	mmeineke	586	// first evolve chi a half step
55	gezelter	574
56			chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
57	mmeineke	586	eta += dt2 * ( instaVol * (instaPress - targetPressure) /
58			(p_convertNkBTtb2));
59	gezelter	574
60			for( i=0; i<nAtoms; i++ ){
61	gezelter	600	atoms[i]->getVel( vel );
62			atoms[i]->getPos( pos );
63			atoms[i]->getFrc( frc );
64	gezelter	574
65	gezelter	600	mass = atoms[i]->getMass();
66	gezelter	574
67	gezelter	600	for (j=0; j < 3; j++) {
68			vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi+eta));
69			rj[j] = pos[j];
70			}
71
72			atoms[i]->setVel( vel );
73
74	gezelter	577	info->wrapVector(rj);
75	gezelter	574
76	gezelter	600	for (j = 0; j < 3; j++)
77			pos[j] += dt * (vel[j] + eta*rj[j]);
78
79
80			atoms[i]->setPos( pos );
81
82
83	gezelter	574	if( atoms[i]->isDirectional() ){
84
85			dAtom = (DirectionalAtom *)atoms[i];
86
87			// get and convert the torque to body frame
88
89	gezelter	600	dAtom->getTrq( Tb );
90	gezelter	574	dAtom->lab2Body( Tb );
91
92			// get the angular momentum, and propagate a half step
93
94	gezelter	600	dAtom->getJ( ji );
95
96			for (j=0; j < 3; j++)
97			ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
98	gezelter	574
99			// use the angular velocities to propagate the rotation matrix a
100			// full time step
101	gezelter	600
102			dAtom->getA(A);
103			dAtom->getI(I);
104
105	gezelter	574	// rotate about the x-axis
106	gezelter	600	angle = dt2 * ji[0] / I[0][0];
107			this->rotate( 1, 2, angle, ji, A );
108
109	gezelter	574	// rotate about the y-axis
110	gezelter	600	angle = dt2 * ji[1] / I[1][1];
111			this->rotate( 2, 0, angle, ji, A );
112	gezelter	574
113			// rotate about the z-axis
114	gezelter	600	angle = dt * ji[2] / I[2][2];
115			this->rotate( 0, 1, angle, ji, A);
116	gezelter	574
117			// rotate about the y-axis
118	gezelter	600	angle = dt2 * ji[1] / I[1][1];
119			this->rotate( 2, 0, angle, ji, A );
120	gezelter	574
121			// rotate about the x-axis
122	gezelter	600	angle = dt2 * ji[0] / I[0][0];
123			this->rotate( 1, 2, angle, ji, A );
124	gezelter	574
125	gezelter	600	dAtom->setJ( ji );
126			dAtom->setA( A );
127			}
128
129	gezelter	574	}
130	gezelter	577	// Scale the box after all the positions have been moved:
131	gezelter	600
132	mmeineke	586	cerr << "eta = " << eta
133			<< "; exp(dteta) = " << exp(etadt) << "\n";
134	gezelter	600
135			info->scaleBox(exp(dt*eta));
136	gezelter	574	}
137
138			void NPTi::moveB( void ){
139	gezelter	600
140			int i, j;
141	gezelter	574	DirectionalAtom* dAtom;
142	gezelter	600	double Tb[3], ji[3];
143			double vel[3], frc[3];
144			double mass;
145
146	gezelter	574	double instaTemp, instaPress, instaVol;
147			double tt2, tb2;
148
149			tt2 = tauThermostat * tauThermostat;
150			tb2 = tauBarostat * tauBarostat;
151
152			instaTemp = tStats->getTemperature();
153			instaPress = tStats->getPressure();
154			instaVol = tStats->getVolume();
155
156			chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
157	mmeineke	586	eta += dt2 * ( instaVol * (instaPress - targetPressure) /
158			(p_convertNkBTtb2));
159	gezelter	574
160			for( i=0; i<nAtoms; i++ ){
161	gezelter	600
162			atoms[i]->getVel( vel );
163			atoms[i]->getFrc( frc );
164
165			mass = atoms[i]->getMass();
166
167	gezelter	574	// velocity half step
168	gezelter	600	for (j=0; j < 3; j++)
169			vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi+eta));
170	gezelter	574
171	gezelter	600	atoms[i]->setVel( vel );
172
173	gezelter	574	if( atoms[i]->isDirectional() ){
174	gezelter	600
175	gezelter	574	dAtom = (DirectionalAtom *)atoms[i];
176	gezelter	600
177			// get and convert the torque to body frame
178
179			dAtom->getTrq( Tb );
180	gezelter	574	dAtom->lab2Body( Tb );
181	gezelter	600
182			// get the angular momentum, and propagate a half step
183
184			dAtom->getJ( ji );
185
186			for (j=0; j < 3; j++)
187			ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
188
189			dAtom->setJ( ji );
190	gezelter	574	}
191			}
192			}
193
194			int NPTi::readyCheck() {
195
196			// First check to see if we have a target temperature.
197			// Not having one is fatal.
198
199			if (!have_target_temp) {
200			sprintf( painCave.errMsg,
201			"NPTi error: You can't use the NPTi integrator\n"
202			" without a targetTemp!\n"
203			);
204			painCave.isFatal = 1;
205			simError();
206			return -1;
207			}
208
209			if (!have_target_pressure) {
210			sprintf( painCave.errMsg,
211			"NPTi error: You can't use the NPTi integrator\n"
212			" without a targetPressure!\n"
213			);
214			painCave.isFatal = 1;
215			simError();
216			return -1;
217			}
218
219			// We must set tauThermostat.
220
221			if (!have_tau_thermostat) {
222			sprintf( painCave.errMsg,
223			"NPTi error: If you use the NPTi\n"
224			" integrator, you must set tauThermostat.\n");
225			painCave.isFatal = 1;
226			simError();
227			return -1;
228			}
229
230			// We must set tauBarostat.
231
232			if (!have_tau_barostat) {
233			sprintf( painCave.errMsg,
234			"NPTi error: If you use the NPTi\n"
235			" integrator, you must set tauBarostat.\n");
236			painCave.isFatal = 1;
237			simError();
238			return -1;
239			}
240
241			// We need NkBT a lot, so just set it here:
242
243			NkBT = (double)info->ndf * kB * targetTemp;
244
245			return 1;
246			}