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
#	Content
1	#include <math.h>
2	#include "Atom.hpp"
3	#include "Molecule.hpp"
4	#include "SimInfo.hpp"
5	#include "Thermo.hpp"
6	#include "ExtendedSystem.hpp"
7	#include "simError.h"
8
9	ExtendedSystem::ExtendedSystem( SimInfo* the_entry_plug ) {
10
11	// get what information we need from the SimInfo object
12
13	entry_plug = the_entry_plug;
14	zeta = 0.0;
15	epsilonDot = 0.0;
16	epsilonDotX = 0.0;
17	epsilonDotY = 0.0;
18	epsilonDotZ = 0.0;
19	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	}
26
27	void ExtendedSystem::NoseHooverNVT( double dt, double ke ){
28
29	// Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697
30
31	int i;
32	double NkBT, zetaScale, ke_temp;
33	double vx, vy, vz, jx, jy, jz;
34	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	DirectionalAtom* dAtom;
38
39	if (this->NVTready()) {
40
41	atoms = entry_plug->atoms;
42
43	ke_temp = ke * e_convert;
44	NkBT = (double)entry_plug->ndf * kB * targetTemp;
45
46	// 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	//std::cerr << "zetaScale = " << zetaScale << "\n";
54
55	// perform thermostat scaling on linear velocities and angular momentum
56	for(i = 0; i < entry_plug->n_atoms; i++){
57
58	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
70	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	}
85	}
86
87
88	void ExtendedSystem::NoseHooverAndersonNPT( double dt,
89	double ke,
90	double p_tensor[9] ) {
91
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	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
102	int i;
103	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
108	if (this->NPTready()) {
109	atoms = entry_plug->atoms;
110
111	p_ext = targetPressure * p_units;
112	p_mol = (p_tensor[0] + p_tensor[4] + p_tensor[8])/3.0;
113
114	entry_plug->getBox(oldBox);
115	volume = oldBox[0]oldBox[1]oldBox[2];
116
117	ke_temp = ke * e_convert;
118	NkBT = (double)entry_plug->ndf * kB * targetTemp;
119
120	// propagate the strain rate
121
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	//std::cerr << "pmol = " << p_mol << " p_ext = " << p_ext << " scale = " << scale << "\n";
128
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	//std::cerr << "zetaScale = " << zetaScale << " epsilonScale = " << epsilonScale << "\n";
148
149	// apply barostating and thermostating to velocities and angular momenta
150	for(i = 0; i < entry_plug->n_atoms; i++){
151
152	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
164	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	}
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	}
278	}
279	}
280
281	void ExtendedSystem::AffineTransform( double oldBox[3], double newBox[3] ){
282
283	int i;
284	double r[3];
285	double boxNum[3];
286	double percentScale[3];
287	double delta[3];
288	double rxi, ryi, rzi;
289
290	molecules = entry_plug->molecules;
291
292	// first determine the scaling factor from the box size change
293	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
297	for (i=0; i < entry_plug->n_mol; i++) {
298
299	molecules[i].getCOM(r);
300
301	// find the minimum image coordinates of the molecular centers of mass:
302
303	boxNum[0] = oldBox[0] * copysign(1.0,r[0]) *
304	(double)(int)(fabs(r[0]/oldBox[0]) + 0.5);
305
306	boxNum[1] = oldBox[1] * copysign(1.0,r[1]) *
307	(double)(int)(fabs(r[1]/oldBox[1]) + 0.5);
308
309	boxNum[2] = oldBox[2] * copysign(1.0,r[2]) *
310	(double)(int)(fabs(r[2]/oldBox[2]) + 0.5);
311
312	rxi = r[0] - boxNum[0];
313	ryi = r[1] - boxNum[1];
314	rzi = r[2] - boxNum[2];
315
316	// update the minimum image coordinates using the scaling factor
317	rxi += rxi*percentScale[0];
318	ryi += ryi*percentScale[1];
319	rzi += rzi*percentScale[2];
320
321	delta[0] = r[0] - (rxi + boxNum[0]);
322	delta[1] = r[1] - (ryi + boxNum[1]);
323	delta[2] = r[2] - (rzi + boxNum[2]);
324
325	molecules[i].moveCOM(delta);
326	}
327	}
328
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	return 1;
359	}
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	return 1;
407	}
408