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 &info ) {

  // get what information we need from the SimInfo object
  
  entry_plug = &info;
  nAtoms = info.n_atoms;
  atoms = info.atoms;
  nMols = info.n_mol;
  molecules = info.molecules;
  zeta = 0.0;
  epsilonDot = 0.0;

}

ExtendedSystem::~ExtendedSystem() {  
}


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
    
  ke_temp = ke * e_convert;
  NkBT = (double)getNDF() * 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;

  // perform thermostat scaling on linear velocities and angular momentum
  for(i = 0; i < 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( n_oriented ){
    
    for( i=0; i < 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

  double p_ext;

  p_ext = targetPressure * p_units;
  p_mol = p_int * p_units;

  getBox(oldBox);

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

  ke_temp = ke * e_convert;
  NkBT = (double)getNDF() * kB * targetTemp;

  // propogate the strain rate

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

  // 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];

  // 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;
  
  // apply barostating and thermostating to velocities and angular momenta
  for(i = 0; i < 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( n_oriented ){
    
    for( i=0; i < 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;
    
  // 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 < nMols; 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:	457
Committed:	Fri Apr 4 19:16:11 2003 UTC (22 years, 7 months ago) by gezelter
File size:	5495 byte(s)
Log Message:	Fixes for ExtendedSystem
#	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			ExtendedSystem::ExtendedSystem( SimInfo &info ) {
9
10			// get what information we need from the SimInfo object
11
12			entry_plug = &info;
13			nAtoms = info.n_atoms;
14			atoms = info.atoms;
15			nMols = info.n_mol;
16			molecules = info.molecules;
17	gezelter	457	zeta = 0.0;
18			epsilonDot = 0.0;
19	gezelter	453
20			}
21
22			ExtendedSystem::~ExtendedSystem() {
23			}
24
25
26	gezelter	457	void ExtendedSystem::NoseHooverNVT( double dt, double ke ){
27	gezelter	453
28			// Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697
29
30	gezelter	454	int i;
31	gezelter	457	double NkBT, zetaScale, ke_temp;
32	gezelter	454	double vx, vy, vz, jx, jy, jz;
33	gezelter	457	const double kB = 8.31451e-7; // boltzmann constant in amuAng^2fs^-2/K
34			const double e_convert = 4.184e-4; // to convert ke from kcal/mol to
35			// amuAng^2fs^-2/K
36
37			ke_temp = ke * e_convert;
38	gezelter	454	NkBT = (double)getNDF() * kB * targetTemp;
39	gezelter	453
40	gezelter	457	// advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin
41	gezelter	453	// qmass is set in the parameter file
42	gezelter	457
43			zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass );
44	gezelter	453	zetaScale = zeta * dt;
45
46			// perform thermostat scaling on linear velocities and angular momentum
47	gezelter	454	for(i = 0; i < n_atoms; i++){
48
49			vx = atoms[i]->get_vx();
50			vy = atoms[i]->get_vy();
51			vz = atoms[i]->get_vz();
52
53	gezelter	457	atoms[i]->set_vx(vx * (1.0 - zetaScale));
54			atoms[i]->set_vy(vy * (1.0 - zetaScale));
55			atoms[i]->set_vz(vz * (1.0 - zetaScale));
56	gezelter	453	}
57	gezelter	454	if( n_oriented ){
58
59			for( i=0; i < n_atoms; i++ ){
60
61			if( atoms[i]->isDirectional() ){
62
63			dAtom = (DirectionalAtom *)atoms[i];
64
65			jx = dAtom->getJx();
66			jy = dAtom->getJy();
67			jz = dAtom->getJz();
68
69	gezelter	457	dAtom->setJx(jx * (1.0 - zetaScale));
70			dAtom->setJy(jy * (1.0 - zetaScale));
71			dAtom->setJz(jz * (1.0 - zetaScale));
72	gezelter	454	}
73			}
74			}
75	gezelter	453	}
76
77
78	gezelter	457	void ExtendedSystem::NoseHooverAndersonNPT( double dt,
79			double ke,
80			double p_int ) {
81	gezelter	453
82			// Basic barostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697
83			// Hoover, Phys.Rev.A, 1986, Vol.34 (3) 2499-2500
84
85	gezelter	457	double oldBox[3];
86			double newBox[3];
87			const double kB = 8.31451e-7; // boltzmann constant in amuAng^2fs^-2/K
88			const double p_units = 6.10192996e-9; // converts atm to amufs^-2Ang^-1
89			const double e_convert = 4.184e-4; // to convert ke from kcal/mol to
90			// amuAng^2fs^-2/K
91	gezelter	453
92	gezelter	457	double p_ext;
93	gezelter	453
94	gezelter	457	p_ext = targetPressure * p_units;
95			p_mol = p_int * p_units;
96	gezelter	453
97	gezelter	457	getBox(oldBox);
98
99			volume = oldBox[0]oldBox[1]oldBox[2];
100
101			ke_temp = ke * e_convert;
102			NkBT = (double)getNDF() * kB * targetTemp;
103
104	gezelter	453	// propogate the strain rate
105
106	gezelter	457	epsilonDot += dt * ((p_mol - p_ext) * volume /
107			(tauRelaxtauRelax kB * targetTemp) );
108	gezelter	453
109			// determine the change in cell volume
110	gezelter	457	scale = pow( (1.0 + dt * 3.0 * epsilonDot), (1.0 / 3.0));
111	gezelter	453
112	gezelter	457	newBox[0] = oldBox[0] * scale;
113			newBox[1] = oldBox[1] * scale;
114			newBox[2] = oldBox[2] * scale;
115			volume = newBox[0]newBox[1]newBox[2];
116	gezelter	453
117			// perform affine transform to update positions with volume fluctuations
118	gezelter	457	this->AffineTransform( oldBox, newBox );
119	gezelter	453
120	gezelter	454	epsilonScale = epsilonDot * dt;
121	gezelter	453
122			// advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin
123			// qmass is set in the parameter file
124	gezelter	457
125			zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass );
126	gezelter	453	zetaScale = zeta * dt;
127
128			// apply barostating and thermostating to velocities and angular momenta
129	gezelter	454	for(i = 0; i < n_atoms; i++){
130
131			vx = atoms[i]->get_vx();
132			vy = atoms[i]->get_vy();
133			vz = atoms[i]->get_vz();
134
135	gezelter	457	atoms[i]->set_vx(vx * (1.0 - zetaScale - epsilonScale));
136			atoms[i]->set_vy(vy * (1.0 - zetaScale - epsilonScale));
137			atoms[i]->set_vz(vz * (1.0 - zetaScale - epsilonScale));
138	gezelter	453	}
139	gezelter	454	if( n_oriented ){
140
141			for( i=0; i < n_atoms; i++ ){
142
143			if( atoms[i]->isDirectional() ){
144
145			dAtom = (DirectionalAtom *)atoms[i];
146
147			jx = dAtom->getJx();
148			jy = dAtom->getJy();
149			jz = dAtom->getJz();
150
151			dAtom->setJx( jx * (1.0 - zetaScale));
152			dAtom->setJy( jy * (1.0 - zetaScale));
153			dAtom->setJz( jz * (1.0 - zetaScale));
154			}
155			}
156			}
157	gezelter	453	}
158
159	gezelter	457	void ExtendedSystem::AffineTransform( double oldBox[3], double newBox[3] ){
160	gezelter	453
161			int i;
162	gezelter	457	double r[3];
163			double boxNum[3];
164			double percentScale[3];
165			double rxi, ryi, rzi;
166	gezelter	453
167			// first determine the scaling factor from the box size change
168	gezelter	457	percentScale[0] = (newBox[0] - oldBox[0]) / oldBox[0];
169			percentScale[1] = (newBox[1] - oldBox[1]) / oldBox[1];
170			percentScale[2] = (newBox[2] - oldBox[2]) / oldBox[2];
171	gezelter	453
172			for (i=0; i < nMols; i++) {
173
174			molecules[i]->getCOM(r);
175
176	gezelter	457	// find the minimum image coordinates of the molecular centers of mass:
177	gezelter	453
178	gezelter	457	boxNum[0] = oldBox[0] * copysign(1.0,r[0]) *
179			(double)(int)(fabs(r[0]/oldBox[0]) + 0.5);
180	gezelter	453
181	gezelter	457	boxNum[1] = oldBox[1] * copysign(1.0,r[1]) *
182			(double)(int)(fabs(r[1]/oldBox[1]) + 0.5);
183	gezelter	453
184	gezelter	457	boxNum[2] = oldBox[2] * copysign(1.0,r[2]) *
185			(double)(int)(fabs(r[2]/oldBox[2]) + 0.5);
186	gezelter	453
187	gezelter	457	rxi = r[0] - boxNum[0];
188			ryi = r[1] - boxNum[1];
189			rzi = r[2] - boxNum[2];
190
191	gezelter	453	// update the minimum image coordinates using the scaling factor
192	gezelter	457	rxi += rxi*percentScale[0];
193			ryi += ryi*percentScale[1];
194			rzi += rzi*percentScale[2];
195	gezelter	453
196	gezelter	457	r[0] = rxi + boxNum[0];
197			r[1] = ryi + boxNum[1];
198			r[2] = rzi + boxNum[2];
199
200			molecules[i]->moveCOM(r);
201	gezelter	453	}
202			}