OOPSE/libmdtools/ExtendedSystem.cpp

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

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;
}

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;    
  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_int ) {

  // 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;
  atoms = entry_plug->atoms;

  p_ext = targetPressure * p_units;
  p_mol = p_int;

  entry_plug->getBox(oldBox);

  volume = oldBox[0]*oldBox[1]*oldBox[2];

  ke_temp = ke * e_convert;
  NkBT = (double)entry_plug->ndf * kB * targetTemp;

  // propogate the strain rate

  epsilonDot +=  dt * ((p_mol - p_ext) * volume / 
                       (tauRelax*tauRelax * kB * targetTemp) );


  std::cerr << "p_mol = " << p_mol << " p_ext = " << p_ext << " volume = " << volume << " tauRelax = " << tauRelax << "\n";


  // determine the change in cell volume
  scale = pow( (1.0 + dt * 3.0 * epsilonDot), (1.0 / 3.0));

  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 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];

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

    molecules[i].moveCOM(r);
  }
}
Revision:	474
Committed:	Mon Apr 7 21:42:19 2003 UTC (21 years, 3 months ago) by gezelter
File size:	6032 byte(s)
Log Message:	Fixes for NPT and NVT
#	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	453
8	gezelter	466	ExtendedSystem::ExtendedSystem( SimInfo* the_entry_plug ) {
9	gezelter	453
10			// get what information we need from the SimInfo object
11
12	gezelter	466	entry_plug = the_entry_plug;
13	gezelter	457	zeta = 0.0;
14			epsilonDot = 0.0;
15	gezelter	453	}
16
17	gezelter	457	void ExtendedSystem::NoseHooverNVT( double dt, double ke ){
18	gezelter	453
19			// Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697
20
21	gezelter	454	int i;
22	gezelter	457	double NkBT, zetaScale, ke_temp;
23	gezelter	454	double vx, vy, vz, jx, jy, jz;
24	gezelter	457	const double kB = 8.31451e-7; // boltzmann constant in amuAng^2fs^-2/K
25			const double e_convert = 4.184e-4; // to convert ke from kcal/mol to
26			// amuAng^2fs^-2/K
27	gezelter	458	DirectionalAtom* dAtom;
28	gezelter	474	atoms = entry_plug->atoms;
29	gezelter	458
30	gezelter	457	ke_temp = ke * e_convert;
31	gezelter	474	NkBT = (double)entry_plug->ndf * kB * targetTemp;
32	gezelter	453
33	gezelter	457	// advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin
34	gezelter	453	// qmass is set in the parameter file
35	gezelter	457
36			zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass );
37	gezelter	471
38	gezelter	453	zetaScale = zeta * dt;
39	gezelter	471
40	gezelter	474	std::cerr << "zetaScale = " << zetaScale << "\n";
41	gezelter	453
42			// perform thermostat scaling on linear velocities and angular momentum
43	gezelter	474	for(i = 0; i < entry_plug->n_atoms; i++){
44	gezelter	454
45			vx = atoms[i]->get_vx();
46			vy = atoms[i]->get_vy();
47			vz = atoms[i]->get_vz();
48	gezelter	474
49	gezelter	457	atoms[i]->set_vx(vx * (1.0 - zetaScale));
50			atoms[i]->set_vy(vy * (1.0 - zetaScale));
51			atoms[i]->set_vz(vz * (1.0 - zetaScale));
52	gezelter	453	}
53	gezelter	474	if( entry_plug->n_oriented ){
54	gezelter	454
55	gezelter	474	for( i=0; i < entry_plug->n_atoms; i++ ){
56	gezelter	454
57			if( atoms[i]->isDirectional() ){
58
59			dAtom = (DirectionalAtom *)atoms[i];
60
61			jx = dAtom->getJx();
62			jy = dAtom->getJy();
63			jz = dAtom->getJz();
64
65	gezelter	457	dAtom->setJx(jx * (1.0 - zetaScale));
66			dAtom->setJy(jy * (1.0 - zetaScale));
67			dAtom->setJz(jz * (1.0 - zetaScale));
68	gezelter	454	}
69			}
70			}
71	gezelter	453	}
72
73
74	gezelter	457	void ExtendedSystem::NoseHooverAndersonNPT( double dt,
75			double ke,
76			double p_int ) {
77	gezelter	453
78			// Basic barostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697
79			// Hoover, Phys.Rev.A, 1986, Vol.34 (3) 2499-2500
80
81	gezelter	457	double oldBox[3];
82			double newBox[3];
83			const double kB = 8.31451e-7; // boltzmann constant in amuAng^2fs^-2/K
84			const double p_units = 6.10192996e-9; // converts atm to amufs^-2Ang^-1
85			const double e_convert = 4.184e-4; // to convert ke from kcal/mol to
86			// amuAng^2fs^-2/K
87	gezelter	453
88	gezelter	474	int i;
89	gezelter	458	double p_ext, zetaScale, epsilonScale, scale, NkBT, ke_temp;
90			double volume, p_mol;
91			double vx, vy, vz, jx, jy, jz;
92			DirectionalAtom* dAtom;
93	gezelter	474	atoms = entry_plug->atoms;
94	gezelter	453
95	gezelter	457	p_ext = targetPressure * p_units;
96	gezelter	474	p_mol = p_int;
97	gezelter	453
98	gezelter	458	entry_plug->getBox(oldBox);
99	gezelter	457
100			volume = oldBox[0]oldBox[1]oldBox[2];
101
102			ke_temp = ke * e_convert;
103	gezelter	474	NkBT = (double)entry_plug->ndf * kB * targetTemp;
104	gezelter	457
105	gezelter	453	// propogate the strain rate
106
107	gezelter	457	epsilonDot += dt * ((p_mol - p_ext) * volume /
108			(tauRelaxtauRelax kB * targetTemp) );
109	gezelter	453
110	gezelter	474
111			std::cerr << "p_mol = " << p_mol << " p_ext = " << p_ext << " volume = " << volume << " tauRelax = " << tauRelax << "\n";
112
113
114	gezelter	453	// determine the change in cell volume
115	gezelter	457	scale = pow( (1.0 + dt * 3.0 * epsilonDot), (1.0 / 3.0));
116	gezelter	453
117	gezelter	457	newBox[0] = oldBox[0] * scale;
118			newBox[1] = oldBox[1] * scale;
119			newBox[2] = oldBox[2] * scale;
120			volume = newBox[0]newBox[1]newBox[2];
121	gezelter	453
122	gezelter	458	entry_plug->setBox(newBox);
123
124	gezelter	453	// perform affine transform to update positions with volume fluctuations
125	gezelter	457	this->AffineTransform( oldBox, newBox );
126	gezelter	453
127	gezelter	454	epsilonScale = epsilonDot * dt;
128	gezelter	453
129			// advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin
130			// qmass is set in the parameter file
131	gezelter	457
132			zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass );
133	gezelter	453	zetaScale = zeta * dt;
134	gezelter	474
135			std::cerr << "zetaScale = " << zetaScale << "epsilonScale = " << epsilonScale << "\n";
136	gezelter	453
137			// apply barostating and thermostating to velocities and angular momenta
138	gezelter	474	for(i = 0; i < entry_plug->n_atoms; i++){
139	gezelter	454
140			vx = atoms[i]->get_vx();
141			vy = atoms[i]->get_vy();
142			vz = atoms[i]->get_vz();
143
144	gezelter	457	atoms[i]->set_vx(vx * (1.0 - zetaScale - epsilonScale));
145			atoms[i]->set_vy(vy * (1.0 - zetaScale - epsilonScale));
146			atoms[i]->set_vz(vz * (1.0 - zetaScale - epsilonScale));
147	gezelter	453	}
148	gezelter	474	if( entry_plug->n_oriented ){
149	gezelter	454
150	gezelter	474	for( i=0; i < entry_plug->n_atoms; i++ ){
151	gezelter	454
152			if( atoms[i]->isDirectional() ){
153
154			dAtom = (DirectionalAtom *)atoms[i];
155
156			jx = dAtom->getJx();
157			jy = dAtom->getJy();
158			jz = dAtom->getJz();
159
160			dAtom->setJx( jx * (1.0 - zetaScale));
161			dAtom->setJy( jy * (1.0 - zetaScale));
162			dAtom->setJz( jz * (1.0 - zetaScale));
163			}
164			}
165			}
166	gezelter	453	}
167
168	gezelter	457	void ExtendedSystem::AffineTransform( double oldBox[3], double newBox[3] ){
169	gezelter	453
170			int i;
171	gezelter	457	double r[3];
172			double boxNum[3];
173			double percentScale[3];
174			double rxi, ryi, rzi;
175	gezelter	474
176			molecules = entry_plug->molecules;
177	gezelter	453
178			// first determine the scaling factor from the box size change
179	gezelter	457	percentScale[0] = (newBox[0] - oldBox[0]) / oldBox[0];
180			percentScale[1] = (newBox[1] - oldBox[1]) / oldBox[1];
181			percentScale[2] = (newBox[2] - oldBox[2]) / oldBox[2];
182	gezelter	453
183	gezelter	474	for (i=0; i < entry_plug->n_mol; i++) {
184	gezelter	453
185	gezelter	458	molecules[i].getCOM(r);
186	gezelter	453
187	gezelter	457	// find the minimum image coordinates of the molecular centers of mass:
188	gezelter	453
189	gezelter	457	boxNum[0] = oldBox[0] * copysign(1.0,r[0]) *
190			(double)(int)(fabs(r[0]/oldBox[0]) + 0.5);
191	gezelter	453
192	gezelter	457	boxNum[1] = oldBox[1] * copysign(1.0,r[1]) *
193			(double)(int)(fabs(r[1]/oldBox[1]) + 0.5);
194	gezelter	453
195	gezelter	457	boxNum[2] = oldBox[2] * copysign(1.0,r[2]) *
196			(double)(int)(fabs(r[2]/oldBox[2]) + 0.5);
197	gezelter	453
198	gezelter	457	rxi = r[0] - boxNum[0];
199			ryi = r[1] - boxNum[1];
200			rzi = r[2] - boxNum[2];
201
202	gezelter	453	// update the minimum image coordinates using the scaling factor
203	gezelter	457	rxi += rxi*percentScale[0];
204			ryi += ryi*percentScale[1];
205			rzi += rzi*percentScale[2];
206	gezelter	453
207	gezelter	457	r[0] = rxi + boxNum[0];
208			r[1] = ryi + boxNum[1];
209			r[2] = rzi + boxNum[2];
210
211	gezelter	458	molecules[i].moveCOM(r);
212	gezelter	453	}
213			}