OOPSE/libmdtools/ExtendedSystem.cpp

#include <math.h>
#include "Atom.hpp"
#include "Molecule.hpp"
#include "SimInfo.hpp"
#include "Thermo.hpp"
#include "ExtendedSystem.hpp"
#include "simError.h"

ExtendedSystem::ExtendedSystem( SimInfo* the_entry_plug ) {

  // get what information we need from the SimInfo object
  
  entry_plug = the_entry_plug;
  zeta = 0.0;
  epsilonDot = 0.0;
  epsilonDotX = 0.0;
  epsilonDotY = 0.0;
  epsilonDotZ = 0.0;  
  have_tau_thermostat = 0;
  have_tau_barostat = 0;
  have_target_temp = 0;
  have_target_pressure = 0; 
  have_qmass = 0;

}

void ExtendedSystem::NoseHooverNVT( double dt, double ke ){

  // Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697
  
  int i;
  double NkBT, zetaScale, ke_temp;
  double vx, vy, vz, jx, jy, jz;
  const double kB = 8.31451e-7;     // boltzmann constant in amu*Ang^2*fs^-2/K
  const double e_convert = 4.184e-4;    // to convert ke from kcal/mol to 
                                        // amu*Ang^2*fs^-2/K
  DirectionalAtom* dAtom;    

  if (this->NVTready()) {

    atoms = entry_plug->atoms;
    
    ke_temp = ke * e_convert;
    NkBT = (double)entry_plug->ndf * kB * targetTemp;
    
    // advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin
    // qmass is set in the parameter file
    
    zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass );
    
    zetaScale = zeta * dt;
    
    //std::cerr << "zetaScale = " << zetaScale << "\n";
    
    // perform thermostat scaling on linear velocities and angular momentum
    for(i = 0; i < entry_plug->n_atoms; i++){
      
      vx = atoms[i]->get_vx();
      vy = atoms[i]->get_vy();
      vz = atoms[i]->get_vz();
      
      atoms[i]->set_vx(vx * (1.0 - zetaScale));
      atoms[i]->set_vy(vy * (1.0 - zetaScale));
      atoms[i]->set_vz(vz * (1.0 - zetaScale));
    }
    if( entry_plug->n_oriented ){
      
      for( i=0; i < entry_plug->n_atoms; i++ ){
        
        if( atoms[i]->isDirectional() ){
          
          dAtom = (DirectionalAtom *)atoms[i];
          
          jx = dAtom->getJx();
          jy = dAtom->getJy();
          jz = dAtom->getJz();
          
          dAtom->setJx(jx * (1.0 - zetaScale));
          dAtom->setJy(jy * (1.0 - zetaScale));
          dAtom->setJz(jz * (1.0 - zetaScale));
        }
      } 
    }
  }
}


void ExtendedSystem::NoseHooverAndersonNPT( double dt, 
                                            double ke, 
                                            double p_tensor[9] ) {

  // Basic barostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697 
  // Hoover, Phys.Rev.A, 1986, Vol.34 (3) 2499-2500

  double oldBox[3];
  double newBox[3];
  const double kB = 8.31451e-7;     // boltzmann constant in amu*Ang^2*fs^-2/K
  const double p_units = 6.10192996e-9; // converts atm to amu*fs^-2*Ang^-1
  const double e_convert = 4.184e-4;    // to convert ke from kcal/mol to 
                                        // amu*Ang^2*fs^-2/K

  int i;
  double p_ext, zetaScale, epsilonScale, scale, NkBT, ke_temp;
  double volume, p_mol;
  double vx, vy, vz, jx, jy, jz;
  DirectionalAtom* dAtom;

  if (this->NPTready()) {
    atoms = entry_plug->atoms;
    
    p_ext = targetPressure * p_units;
    p_mol = (p_tensor[0] + p_tensor[4] + p_tensor[8])/3.0;
   
    entry_plug->getBox(oldBox);
    volume = oldBox[0]*oldBox[1]*oldBox[2];
    
    ke_temp = ke * e_convert;
    NkBT = (double)entry_plug->ndf * kB * targetTemp;
    
    // propagate the strain rate
    
    epsilonDot +=  dt * ((p_mol - p_ext) * volume / 
                         (tauBarostat*tauBarostat * kB * targetTemp) );
    
    // determine the change in cell volume
    scale = pow( (1.0 + dt * 3.0 * epsilonDot), (1.0 / 3.0));
    //std::cerr << "pmol = " << p_mol << " p_ext = " << p_ext << " scale = " << scale << "\n"; 
    
    newBox[0] = oldBox[0] * scale;
    newBox[1] = oldBox[1] * scale;
    newBox[2] = oldBox[2] * scale;
    volume = newBox[0]*newBox[1]*newBox[2];
    
    entry_plug->setBox(newBox);
    
    // perform affine transform to update positions with volume fluctuations
    this->AffineTransform( oldBox, newBox );
    
    epsilonScale = epsilonDot * dt;
    
    // advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin 
    // qmass is set in the parameter file
    
    zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass );
    zetaScale = zeta * dt;
    
    //std::cerr << "zetaScale = " << zetaScale << " epsilonScale = " << epsilonScale <<  "\n";
    
  // apply barostating and thermostating to velocities and angular momenta
    for(i = 0; i < entry_plug->n_atoms; i++){
      
      vx = atoms[i]->get_vx();
      vy = atoms[i]->get_vy();
      vz = atoms[i]->get_vz();
      
      atoms[i]->set_vx(vx * (1.0 - zetaScale - epsilonScale));
      atoms[i]->set_vy(vy * (1.0 - zetaScale - epsilonScale));
      atoms[i]->set_vz(vz * (1.0 - zetaScale - epsilonScale));
    }
    if( entry_plug->n_oriented ){
      
      for( i=0; i < entry_plug->n_atoms; i++ ){
        
        if( atoms[i]->isDirectional() ){
          
          dAtom = (DirectionalAtom *)atoms[i];
          
          jx = dAtom->getJx();
          jy = dAtom->getJy();
          jz = dAtom->getJz();
          
          dAtom->setJx( jx * (1.0 - zetaScale));
          dAtom->setJy( jy * (1.0 - zetaScale));
          dAtom->setJz( jz * (1.0 - zetaScale));
        }
      } 
    }
  }
}


void ExtendedSystem::ConstantStress( double dt, 
                                     double ke, 
                                     double p_tensor[9] ) {

  double oldBox[3];
  double newBox[3];
  const double kB = 8.31451e-7;     // boltzmann constant in amu*Ang^2*fs^-2/K
  const double p_units = 6.10192996e-9; // converts atm to amu*fs^-2*Ang^-1
  const double e_convert = 4.184e-4;    // to convert ke from kcal/mol to 
                                        // amu*Ang^2*fs^-2/K

  int i;
  double p_ext, zetaScale, epsilonScale, scale, NkBT, ke_temp;
  double pX_ext, pY_ext, pZ_ext;
  double volume, p_mol;
  double vx, vy, vz, jx, jy, jz;
  DirectionalAtom* dAtom;

  if (this->NPTready()) {
    atoms = entry_plug->atoms;
    
    p_ext = targetPressure * p_units;

    pX_ext = p_ext / 3.0;
    pY_ext = p_ext / 3.0;
    pZ_ext = p_ext / 3.0;
   
    entry_plug->getBox(oldBox);
    volume = oldBox[0]*oldBox[1]*oldBox[2];
    
    ke_temp = ke * e_convert;
    NkBT = (double)entry_plug->ndf * kB * targetTemp;
    
    // propagate the strain rate
    
    epsilonDotX +=  dt * ((p_tensor[0] - pX_ext) * volume / 
                          (tauBarostat*tauBarostat * kB * targetTemp) );
    epsilonDotY +=  dt * ((p_tensor[4] - pY_ext) * volume / 
                          (tauBarostat*tauBarostat * kB * targetTemp) );
    epsilonDotZ +=  dt * ((p_tensor[8] - pZ_ext) * volume / 
                          (tauBarostat*tauBarostat * kB * targetTemp) );
    
    // determine the change in cell volume

    //scale = pow( (1.0 + dt * 3.0 * (epsilonDot), (1.0 / 3.0));
    //std::cerr << "pmol = " << p_mol << " p_ext = " << p_ext << " scale = " << scale << "\n"; 
    
    newBox[0] = oldBox[0] * scale;
    newBox[1] = oldBox[1] * scale;
    newBox[2] = oldBox[2] * scale;
    volume = newBox[0]*newBox[1]*newBox[2];
    
    entry_plug->setBox(newBox);
    
    // perform affine transform to update positions with volume fluctuations
    this->AffineTransform( oldBox, newBox );
    
    epsilonScale = epsilonDot * dt;
    
    // advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin 
    // qmass is set in the parameter file
    
    zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass );
    zetaScale = zeta * dt;
    
    //std::cerr << "zetaScale = " << zetaScale << " epsilonScale = " << epsilonScale <<  "\n";
    
  // apply barostating and thermostating to velocities and angular momenta
    for(i = 0; i < entry_plug->n_atoms; i++){
      
      vx = atoms[i]->get_vx();
      vy = atoms[i]->get_vy();
      vz = atoms[i]->get_vz();
      
      atoms[i]->set_vx(vx * (1.0 - zetaScale - epsilonScale));
      atoms[i]->set_vy(vy * (1.0 - zetaScale - epsilonScale));
      atoms[i]->set_vz(vz * (1.0 - zetaScale - epsilonScale));
    }
    if( entry_plug->n_oriented ){
      
      for( i=0; i < entry_plug->n_atoms; i++ ){
        
        if( atoms[i]->isDirectional() ){
          
          dAtom = (DirectionalAtom *)atoms[i];
          
          jx = dAtom->getJx();
          jy = dAtom->getJy();
          jz = dAtom->getJz();
          
          dAtom->setJx( jx * (1.0 - zetaScale));
          dAtom->setJy( jy * (1.0 - zetaScale));
          dAtom->setJz( jz * (1.0 - zetaScale));
        }
      } 
    }
  }
}

void ExtendedSystem::AffineTransform( double oldBox[3], double newBox[3] ){

  int i;
  double r[3];
  double boxNum[3];
  double percentScale[3];
  double delta[3];
  double rxi, ryi, rzi;

  molecules = entry_plug->molecules;
    
  // first determine the scaling factor from the box size change
  percentScale[0] = (newBox[0] - oldBox[0]) / oldBox[0];
  percentScale[1] = (newBox[1] - oldBox[1]) / oldBox[1];
  percentScale[2] = (newBox[2] - oldBox[2]) / oldBox[2];
  
  for (i=0; i < entry_plug->n_mol; i++) {
    
    molecules[i].getCOM(r);

    // find the minimum image coordinates of the molecular centers of mass:    
    
    boxNum[0] = oldBox[0] * copysign(1.0,r[0]) * 
      (double)(int)(fabs(r[0]/oldBox[0]) + 0.5);

    boxNum[1] = oldBox[1] * copysign(1.0,r[1]) * 
      (double)(int)(fabs(r[1]/oldBox[1]) + 0.5);

    boxNum[2] = oldBox[2] * copysign(1.0,r[2]) * 
      (double)(int)(fabs(r[2]/oldBox[2]) + 0.5);

    rxi = r[0] - boxNum[0];
    ryi = r[1] - boxNum[1];
    rzi = r[2] - boxNum[2];

    // update the minimum image coordinates using the scaling factor
    rxi += rxi*percentScale[0];
    ryi += ryi*percentScale[1];
    rzi += rzi*percentScale[2];

    delta[0] = r[0] - (rxi + boxNum[0]);
    delta[1] = r[1] - (ryi + boxNum[1]);
    delta[2] = r[2] - (rzi + boxNum[2]);

    molecules[i].moveCOM(delta);
  }
}

short int ExtendedSystem::NVTready() {
  const double kB = 8.31451e-7;     // boltzmann constant in amu*Ang^2*fs^-2/K
  double NkBT;

  if (!have_target_temp) {
    sprintf( painCave.errMsg,
             "ExtendedSystem error: You can't use NVT without a targetTemp!\n"
             );
    painCave.isFatal = 1;
    simError();
    return -1;
  }
    
  if (!have_qmass) {
    if (have_tau_thermostat) {

      NkBT = (double)entry_plug->ndf * kB * targetTemp;
      std::cerr << "Setting qMass = " << tauThermostat * NkBT << "\n";
      this->setQmass(tauThermostat * NkBT);

    } else {
      sprintf( painCave.errMsg,
               "ExtendedSystem error: If you use the constant temperature\n"
               "    ensemble, you must set either tauThermostat or qMass.\n");
      painCave.isFatal = 1;
      simError();
    }
  }

  return 1;
}

short int ExtendedSystem::NPTready() {
  const double kB = 8.31451e-7;     // boltzmann constant in amu*Ang^2*fs^-2/K
  double NkBT;

  if (!have_target_temp) {
    sprintf( painCave.errMsg,
             "ExtendedSystem error: You can't use NPT without a targetTemp!\n"
             );
    painCave.isFatal = 1;
    simError();
    return -1;
  }

  if (!have_target_pressure) {
    sprintf( painCave.errMsg,
             "ExtendedSystem error: You can't use NPT without a targetPressure!\n"
             );
    painCave.isFatal = 1;
    simError();
    return -1;
  }
    
  if (!have_tau_barostat) {
    sprintf( painCave.errMsg,
             "ExtendedSystem error: If you use the NPT\n"
             "    ensemble, you must set tauBarostat.\n");
    painCave.isFatal = 1;
    simError();
  }

  if (!have_qmass) {
    if (have_tau_thermostat) {

      NkBT = (double)entry_plug->ndf * kB * targetTemp;
      std::cerr << "Setting qMass = " << tauThermostat * NkBT << "\n";
      this->setQmass(tauThermostat * NkBT);

    } else {
      sprintf( painCave.errMsg,
               "ExtendedSystem error: If you use the NPT\n"
               "    ensemble, you must set either tauThermostat or qMass.\n");
      painCave.isFatal = 1;
      simError();
    }  
  }
  return 1;
}
  
Revision:	488
Committed:	Thu Apr 10 16:35:31 2003 UTC (21 years, 3 months ago) by gezelter
File size:	12135 byte(s)
Log Message:	Working on ConstantStress
#	User	Rev	Content
1	gezelter	453	#include <math.h>
2	gezelter	454	#include "Atom.hpp"
3			#include "Molecule.hpp"
4			#include "SimInfo.hpp"
5			#include "Thermo.hpp"
6			#include "ExtendedSystem.hpp"
7	gezelter	481	#include "simError.h"
8	gezelter	453
9	gezelter	466	ExtendedSystem::ExtendedSystem( SimInfo* the_entry_plug ) {
10	gezelter	453
11			// get what information we need from the SimInfo object
12
13	gezelter	466	entry_plug = the_entry_plug;
14	gezelter	457	zeta = 0.0;
15			epsilonDot = 0.0;
16	gezelter	488	epsilonDotX = 0.0;
17			epsilonDotY = 0.0;
18			epsilonDotZ = 0.0;
19	gezelter	481	have_tau_thermostat = 0;
20			have_tau_barostat = 0;
21			have_target_temp = 0;
22			have_target_pressure = 0;
23			have_qmass = 0;
24
25	gezelter	453	}
26
27	gezelter	457	void ExtendedSystem::NoseHooverNVT( double dt, double ke ){
28	gezelter	453
29			// Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697
30
31	gezelter	454	int i;
32	gezelter	457	double NkBT, zetaScale, ke_temp;
33	gezelter	454	double vx, vy, vz, jx, jy, jz;
34	gezelter	457	const double kB = 8.31451e-7; // boltzmann constant in amuAng^2fs^-2/K
35			const double e_convert = 4.184e-4; // to convert ke from kcal/mol to
36			// amuAng^2fs^-2/K
37	gezelter	458	DirectionalAtom* dAtom;
38
39	gezelter	481	if (this->NVTready()) {
40	gezelter	453
41	gezelter	481	atoms = entry_plug->atoms;
42	gezelter	454
43	gezelter	481	ke_temp = ke * e_convert;
44			NkBT = (double)entry_plug->ndf * kB * targetTemp;
45	gezelter	454
46	gezelter	481	// advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin
47			// qmass is set in the parameter file
48
49			zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass );
50
51			zetaScale = zeta * dt;
52
53	gezelter	484	//std::cerr << "zetaScale = " << zetaScale << "\n";
54	gezelter	481
55			// perform thermostat scaling on linear velocities and angular momentum
56			for(i = 0; i < entry_plug->n_atoms; i++){
57	gezelter	454
58	gezelter	481	vx = atoms[i]->get_vx();
59			vy = atoms[i]->get_vy();
60			vz = atoms[i]->get_vz();
61
62			atoms[i]->set_vx(vx * (1.0 - zetaScale));
63			atoms[i]->set_vy(vy * (1.0 - zetaScale));
64			atoms[i]->set_vz(vz * (1.0 - zetaScale));
65			}
66			if( entry_plug->n_oriented ){
67
68			for( i=0; i < entry_plug->n_atoms; i++ ){
69	gezelter	454
70	gezelter	481	if( atoms[i]->isDirectional() ){
71
72			dAtom = (DirectionalAtom *)atoms[i];
73
74			jx = dAtom->getJx();
75			jy = dAtom->getJy();
76			jz = dAtom->getJz();
77
78			dAtom->setJx(jx * (1.0 - zetaScale));
79			dAtom->setJy(jy * (1.0 - zetaScale));
80			dAtom->setJz(jz * (1.0 - zetaScale));
81			}
82			}
83			}
84	gezelter	454	}
85	gezelter	453	}
86
87
88	gezelter	457	void ExtendedSystem::NoseHooverAndersonNPT( double dt,
89			double ke,
90	gezelter	483	double p_tensor[9] ) {
91	gezelter	453
92			// Basic barostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697
93			// Hoover, Phys.Rev.A, 1986, Vol.34 (3) 2499-2500
94
95	gezelter	457	double oldBox[3];
96			double newBox[3];
97			const double kB = 8.31451e-7; // boltzmann constant in amuAng^2fs^-2/K
98			const double p_units = 6.10192996e-9; // converts atm to amufs^-2Ang^-1
99			const double e_convert = 4.184e-4; // to convert ke from kcal/mol to
100			// amuAng^2fs^-2/K
101	gezelter	453
102	gezelter	474	int i;
103	gezelter	458	double p_ext, zetaScale, epsilonScale, scale, NkBT, ke_temp;
104			double volume, p_mol;
105			double vx, vy, vz, jx, jy, jz;
106			DirectionalAtom* dAtom;
107	gezelter	453
108	gezelter	481	if (this->NPTready()) {
109			atoms = entry_plug->atoms;
110	gezelter	454
111	gezelter	481	p_ext = targetPressure * p_units;
112	gezelter	483	p_mol = (p_tensor[0] + p_tensor[4] + p_tensor[8])/3.0;
113
114	gezelter	481	entry_plug->getBox(oldBox);
115			volume = oldBox[0]oldBox[1]oldBox[2];
116	gezelter	454
117	gezelter	481	ke_temp = ke * e_convert;
118			NkBT = (double)entry_plug->ndf * kB * targetTemp;
119
120	gezelter	483	// propagate the strain rate
121	gezelter	481
122			epsilonDot += dt * ((p_mol - p_ext) * volume /
123			(tauBarostattauBarostat kB * targetTemp) );
124
125			// determine the change in cell volume
126			scale = pow( (1.0 + dt * 3.0 * epsilonDot), (1.0 / 3.0));
127	gezelter	484	//std::cerr << "pmol = " << p_mol << " p_ext = " << p_ext << " scale = " << scale << "\n";
128	gezelter	481
129			newBox[0] = oldBox[0] * scale;
130			newBox[1] = oldBox[1] * scale;
131			newBox[2] = oldBox[2] * scale;
132			volume = newBox[0]newBox[1]newBox[2];
133
134			entry_plug->setBox(newBox);
135
136			// perform affine transform to update positions with volume fluctuations
137			this->AffineTransform( oldBox, newBox );
138
139			epsilonScale = epsilonDot * dt;
140
141			// advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin
142			// qmass is set in the parameter file
143
144			zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass );
145			zetaScale = zeta * dt;
146
147	gezelter	484	//std::cerr << "zetaScale = " << zetaScale << " epsilonScale = " << epsilonScale << "\n";
148	gezelter	481
149			// apply barostating and thermostating to velocities and angular momenta
150			for(i = 0; i < entry_plug->n_atoms; i++){
151	gezelter	454
152	gezelter	481	vx = atoms[i]->get_vx();
153			vy = atoms[i]->get_vy();
154			vz = atoms[i]->get_vz();
155
156			atoms[i]->set_vx(vx * (1.0 - zetaScale - epsilonScale));
157			atoms[i]->set_vy(vy * (1.0 - zetaScale - epsilonScale));
158			atoms[i]->set_vz(vz * (1.0 - zetaScale - epsilonScale));
159			}
160			if( entry_plug->n_oriented ){
161
162			for( i=0; i < entry_plug->n_atoms; i++ ){
163	gezelter	454
164	gezelter	481	if( atoms[i]->isDirectional() ){
165
166			dAtom = (DirectionalAtom *)atoms[i];
167
168			jx = dAtom->getJx();
169			jy = dAtom->getJy();
170			jz = dAtom->getJz();
171
172			dAtom->setJx( jx * (1.0 - zetaScale));
173			dAtom->setJy( jy * (1.0 - zetaScale));
174			dAtom->setJz( jz * (1.0 - zetaScale));
175			}
176			}
177	gezelter	488	}
178			}
179			}
180
181
182			void ExtendedSystem::ConstantStress( double dt,
183			double ke,
184			double p_tensor[9] ) {
185
186			double oldBox[3];
187			double newBox[3];
188			const double kB = 8.31451e-7; // boltzmann constant in amuAng^2fs^-2/K
189			const double p_units = 6.10192996e-9; // converts atm to amufs^-2Ang^-1
190			const double e_convert = 4.184e-4; // to convert ke from kcal/mol to
191			// amuAng^2fs^-2/K
192
193			int i;
194			double p_ext, zetaScale, epsilonScale, scale, NkBT, ke_temp;
195			double pX_ext, pY_ext, pZ_ext;
196			double volume, p_mol;
197			double vx, vy, vz, jx, jy, jz;
198			DirectionalAtom* dAtom;
199
200			if (this->NPTready()) {
201			atoms = entry_plug->atoms;
202
203			p_ext = targetPressure * p_units;
204
205			pX_ext = p_ext / 3.0;
206			pY_ext = p_ext / 3.0;
207			pZ_ext = p_ext / 3.0;
208
209			entry_plug->getBox(oldBox);
210			volume = oldBox[0]oldBox[1]oldBox[2];
211
212			ke_temp = ke * e_convert;
213			NkBT = (double)entry_plug->ndf * kB * targetTemp;
214
215			// propagate the strain rate
216
217			epsilonDotX += dt * ((p_tensor[0] - pX_ext) * volume /
218			(tauBarostattauBarostat kB * targetTemp) );
219			epsilonDotY += dt * ((p_tensor[4] - pY_ext) * volume /
220			(tauBarostattauBarostat kB * targetTemp) );
221			epsilonDotZ += dt * ((p_tensor[8] - pZ_ext) * volume /
222			(tauBarostattauBarostat kB * targetTemp) );
223
224			// determine the change in cell volume
225
226			//scale = pow( (1.0 + dt * 3.0 * (epsilonDot), (1.0 / 3.0));
227			//std::cerr << "pmol = " << p_mol << " p_ext = " << p_ext << " scale = " << scale << "\n";
228
229			newBox[0] = oldBox[0] * scale;
230			newBox[1] = oldBox[1] * scale;
231			newBox[2] = oldBox[2] * scale;
232			volume = newBox[0]newBox[1]newBox[2];
233
234			entry_plug->setBox(newBox);
235
236			// perform affine transform to update positions with volume fluctuations
237			this->AffineTransform( oldBox, newBox );
238
239			epsilonScale = epsilonDot * dt;
240
241			// advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin
242			// qmass is set in the parameter file
243
244			zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass );
245			zetaScale = zeta * dt;
246
247			//std::cerr << "zetaScale = " << zetaScale << " epsilonScale = " << epsilonScale << "\n";
248
249			// apply barostating and thermostating to velocities and angular momenta
250			for(i = 0; i < entry_plug->n_atoms; i++){
251
252			vx = atoms[i]->get_vx();
253			vy = atoms[i]->get_vy();
254			vz = atoms[i]->get_vz();
255
256			atoms[i]->set_vx(vx * (1.0 - zetaScale - epsilonScale));
257			atoms[i]->set_vy(vy * (1.0 - zetaScale - epsilonScale));
258			atoms[i]->set_vz(vz * (1.0 - zetaScale - epsilonScale));
259			}
260			if( entry_plug->n_oriented ){
261
262			for( i=0; i < entry_plug->n_atoms; i++ ){
263
264			if( atoms[i]->isDirectional() ){
265
266			dAtom = (DirectionalAtom *)atoms[i];
267
268			jx = dAtom->getJx();
269			jy = dAtom->getJy();
270			jz = dAtom->getJz();
271
272			dAtom->setJx( jx * (1.0 - zetaScale));
273			dAtom->setJy( jy * (1.0 - zetaScale));
274			dAtom->setJz( jz * (1.0 - zetaScale));
275			}
276			}
277	gezelter	481	}
278	gezelter	454	}
279	gezelter	453	}
280
281	gezelter	457	void ExtendedSystem::AffineTransform( double oldBox[3], double newBox[3] ){
282	gezelter	453
283			int i;
284	gezelter	457	double r[3];
285			double boxNum[3];
286			double percentScale[3];
287	gezelter	476	double delta[3];
288	gezelter	457	double rxi, ryi, rzi;
289	gezelter	474
290			molecules = entry_plug->molecules;
291	gezelter	453
292			// first determine the scaling factor from the box size change
293	gezelter	457	percentScale[0] = (newBox[0] - oldBox[0]) / oldBox[0];
294			percentScale[1] = (newBox[1] - oldBox[1]) / oldBox[1];
295			percentScale[2] = (newBox[2] - oldBox[2]) / oldBox[2];
296	gezelter	453
297	gezelter	474	for (i=0; i < entry_plug->n_mol; i++) {
298	gezelter	453
299	gezelter	458	molecules[i].getCOM(r);
300	gezelter	475
301	gezelter	457	// find the minimum image coordinates of the molecular centers of mass:
302	gezelter	453
303	gezelter	457	boxNum[0] = oldBox[0] * copysign(1.0,r[0]) *
304			(double)(int)(fabs(r[0]/oldBox[0]) + 0.5);
305	gezelter	453
306	gezelter	457	boxNum[1] = oldBox[1] * copysign(1.0,r[1]) *
307			(double)(int)(fabs(r[1]/oldBox[1]) + 0.5);
308	gezelter	453
309	gezelter	457	boxNum[2] = oldBox[2] * copysign(1.0,r[2]) *
310			(double)(int)(fabs(r[2]/oldBox[2]) + 0.5);
311	gezelter	453
312	gezelter	457	rxi = r[0] - boxNum[0];
313			ryi = r[1] - boxNum[1];
314			rzi = r[2] - boxNum[2];
315
316	gezelter	453	// update the minimum image coordinates using the scaling factor
317	gezelter	457	rxi += rxi*percentScale[0];
318			ryi += ryi*percentScale[1];
319			rzi += rzi*percentScale[2];
320	gezelter	453
321	gezelter	476	delta[0] = r[0] - (rxi + boxNum[0]);
322			delta[1] = r[1] - (ryi + boxNum[1]);
323			delta[2] = r[2] - (rzi + boxNum[2]);
324	gezelter	457
325	gezelter	476	molecules[i].moveCOM(delta);
326	gezelter	453	}
327			}
328	gezelter	481
329			short int ExtendedSystem::NVTready() {
330			const double kB = 8.31451e-7; // boltzmann constant in amuAng^2fs^-2/K
331			double NkBT;
332
333			if (!have_target_temp) {
334			sprintf( painCave.errMsg,
335			"ExtendedSystem error: You can't use NVT without a targetTemp!\n"
336			);
337			painCave.isFatal = 1;
338			simError();
339			return -1;
340			}
341
342			if (!have_qmass) {
343			if (have_tau_thermostat) {
344
345			NkBT = (double)entry_plug->ndf * kB * targetTemp;
346			std::cerr << "Setting qMass = " << tauThermostat * NkBT << "\n";
347			this->setQmass(tauThermostat * NkBT);
348
349			} else {
350			sprintf( painCave.errMsg,
351			"ExtendedSystem error: If you use the constant temperature\n"
352			" ensemble, you must set either tauThermostat or qMass.\n");
353			painCave.isFatal = 1;
354			simError();
355			}
356			}
357
358	gezelter	483	return 1;
359	gezelter	481	}
360
361			short int ExtendedSystem::NPTready() {
362			const double kB = 8.31451e-7; // boltzmann constant in amuAng^2fs^-2/K
363			double NkBT;
364
365			if (!have_target_temp) {
366			sprintf( painCave.errMsg,
367			"ExtendedSystem error: You can't use NPT without a targetTemp!\n"
368			);
369			painCave.isFatal = 1;
370			simError();
371			return -1;
372			}
373
374			if (!have_target_pressure) {
375			sprintf( painCave.errMsg,
376			"ExtendedSystem error: You can't use NPT without a targetPressure!\n"
377			);
378			painCave.isFatal = 1;
379			simError();
380			return -1;
381			}
382
383			if (!have_tau_barostat) {
384			sprintf( painCave.errMsg,
385			"ExtendedSystem error: If you use the NPT\n"
386			" ensemble, you must set tauBarostat.\n");
387			painCave.isFatal = 1;
388			simError();
389			}
390
391			if (!have_qmass) {
392			if (have_tau_thermostat) {
393
394			NkBT = (double)entry_plug->ndf * kB * targetTemp;
395			std::cerr << "Setting qMass = " << tauThermostat * NkBT << "\n";
396			this->setQmass(tauThermostat * NkBT);
397
398			} else {
399			sprintf( painCave.errMsg,
400			"ExtendedSystem error: If you use the NPT\n"
401			" ensemble, you must set either tauThermostat or qMass.\n");
402			painCave.isFatal = 1;
403			simError();
404			}
405			}
406	gezelter	483	return 1;
407	gezelter	481	}
408