1 |
gezelter |
445 |
#include <math.h> |
2 |
|
|
|
3 |
|
|
|
4 |
|
|
void NVT::nose_hoover_nvt( double ke, double dt, double temp ){ |
5 |
|
|
|
6 |
|
|
// Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697 |
7 |
|
|
|
8 |
|
|
int i, j, degrees_freedom; |
9 |
|
|
double ke, dt, temp, kB; |
10 |
|
|
double keconverter, NkBT, zetaScale, ke_temp; |
11 |
|
|
double vxi, vyi, vzi, jxi, jyi, jzi; |
12 |
|
|
|
13 |
|
|
degrees_freedom = 6*nmol; // number of degrees of freedom for the system |
14 |
|
|
kB = 8.31451e-7; // boltzmann constant in amu*Ang^2*fs^-2/K |
15 |
|
|
keconverter = 4.184e-4; // to convert ke from kcal/mol to amu*Ang^2*fs^-2 / K |
16 |
|
|
|
17 |
|
|
ke_temp = ke * keconverter; |
18 |
|
|
NkBT = degrees_freedom*kB*temp; |
19 |
|
|
|
20 |
|
|
// advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin & |
21 |
|
|
// qmass is set in the parameter file |
22 |
|
|
zeta = zeta + dt*((ke_temp*2 - NkBT)/qmass); |
23 |
|
|
zetaScale = zeta * dt; |
24 |
|
|
|
25 |
|
|
// perform thermostat scaling on linear velocities and angular momentum |
26 |
|
|
for(i = 0, i < nmol; i++ ) { |
27 |
|
|
vxi = vx(i)*zetaScale; |
28 |
|
|
vyi = vy(i)*zetaScale; |
29 |
|
|
vzi = vz(i)*zetaScale; |
30 |
|
|
jxi = jx(i)*zetaScale; |
31 |
|
|
jyi = jy(i)*zetaScale; |
32 |
|
|
jzi = jz(i)*zetaScale; |
33 |
|
|
|
34 |
|
|
vx(i) = vx(i) - vxi; |
35 |
|
|
vy(i) = vy(i) - vyi; |
36 |
|
|
vz(i) = vz(i) - vzi; |
37 |
|
|
jx(i) = jx(i) - jxi; |
38 |
|
|
jy(i) = jy(i) - jyi; |
39 |
|
|
jz(i) = jz(i) - jzi; |
40 |
|
|
} |
41 |
|
|
} |
42 |
|
|
|
43 |
|
|
|
44 |
|
|
void NVT::nose_hoover_anderson_npt(double pressure, double ke, double dt, |
45 |
|
|
double temp ) { |
46 |
|
|
|
47 |
|
|
// Basic barostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697 |
48 |
|
|
// Hoover, Phys.Rev.A, 1986, Vol.34 (3) 2499-2500 |
49 |
|
|
|
50 |
|
|
int i, j, degrees_freedom; |
51 |
|
|
double pressure, dt, temp, pressure_units, epsilonScale; |
52 |
|
|
double ke, kB, vxi, vyi, vzi, pressure_ext; |
53 |
|
|
double boxx_old, boxy_old, boxz_old; |
54 |
|
|
double keconverter, NkBT, zetaScale, ke_temp; |
55 |
|
|
double jxi, jyi, jzi, scale; |
56 |
|
|
|
57 |
|
|
kB = 8.31451e-7; // boltzmann constant in amu*Ang^2*fs^-2/K |
58 |
|
|
pressure_units = 6.10192996e-9; // converts atm to amu*fs^-2*Ang^-1 |
59 |
|
|
degrees_freedom = 6*nmol; // number of degrees of freedom for the system |
60 |
|
|
keconverter = 4.184e-4; // to convert ke from kcal/mol to amu*Ang^2*fs^-2/K |
61 |
|
|
|
62 |
|
|
pressure_ext = pressure * pressure_units; |
63 |
|
|
volume = boxx*boxy*boxz; |
64 |
|
|
ke_temp = ke * keconverter; |
65 |
|
|
NkBT = degrees_freedom*kB*temp; |
66 |
|
|
|
67 |
|
|
// propogate the strain rate |
68 |
|
|
epsilon_dot = epsilon_dot + dt*( (p_mol - pressure_ext)*volume |
69 |
|
|
/ (tau_relax*tau_relax * kB * temp) ); |
70 |
|
|
|
71 |
|
|
// determine the change in cell volume |
72 |
|
|
scale = (1.0d0 + dt*3.0d0*epsilon_dot)**(1.0d0/3.0d0); |
73 |
|
|
|
74 |
|
|
volume = volume * scale**3; |
75 |
|
|
|
76 |
|
|
// save old lengths and update box size |
77 |
|
|
boxx_old = boxx; |
78 |
|
|
boxy_old = boxy; |
79 |
|
|
boxz_old = boxz; |
80 |
|
|
boxx = boxx_old*scale; |
81 |
|
|
boxy = boxy_old*scale; |
82 |
|
|
boxz = boxz_old*scale; |
83 |
|
|
|
84 |
|
|
epsilonScale = epsilon_dot * dt; |
85 |
|
|
|
86 |
|
|
// advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin |
87 |
|
|
// qmass is set in the parameter file |
88 |
|
|
zeta = zeta + dt*((ke_temp*2 - NkBT)/qmass); |
89 |
|
|
zetaScale = zeta * dt; |
90 |
|
|
|
91 |
|
|
// apply barostating and thermostating to velocities and angular momenta |
92 |
|
|
|
93 |
|
|
for (i=0; i < nmol; i++) { |
94 |
|
|
|
95 |
|
|
vxi = vx(i)*epsilonScale; |
96 |
|
|
vyi = vy(i)*epsilonScale; |
97 |
|
|
vzi = vz(i)*epsilonScale; |
98 |
|
|
vxi = vxi + vx(i)*zetaScale; |
99 |
|
|
vyi = vyi + vy(i)*zetaScale; |
100 |
|
|
vzi = vzi + vz(i)*zetaScale; |
101 |
|
|
jxi = jx(i)*zetaScale; |
102 |
|
|
jyi = jy(i)*zetaScale; |
103 |
|
|
jzi = jz(i)*zetaScale; |
104 |
|
|
|
105 |
|
|
vx(i) = vx(i) - vxi; |
106 |
|
|
vy(i) = vy(i) - vyi; |
107 |
|
|
vz(i) = vz(i) - vzi; |
108 |
|
|
jx(i) = jx(i) - jxi; |
109 |
|
|
jy(i) = jy(i) - jyi; |
110 |
|
|
jz(i) = jz(i) - jzi; |
111 |
|
|
} |
112 |
|
|
|
113 |
|
|
// perform affine transform to update positions with volume fluctuations |
114 |
|
|
affine_transform( boxx_old, boxy_old, boxz_old ); |
115 |
|
|
} |
116 |
|
|
|
117 |
|
|
void NVT::affine_transform( double boxx_old, double boxy_old, double boxz_old ){ |
118 |
|
|
|
119 |
|
|
int i; |
120 |
|
|
double boxx_old, boxy_old, boxz_old, percentScale; |
121 |
|
|
double boxx_num, boxy_num, boxz_num, rxi, ryi, rzi; |
122 |
|
|
|
123 |
|
|
// first determine the scaling factor from the box size change |
124 |
|
|
percentScale = (boxx - boxx_old)/boxx_old; |
125 |
|
|
|
126 |
|
|
|
127 |
|
|
for (i=0; i < nmol; i++) { |
128 |
|
|
|
129 |
|
|
// find the minimum image coordinates |
130 |
|
|
boxx_num = boxx_old*dsign(1.0d0,rx(i))*int(abs(rx(i)/boxx_old)+0.5d0); |
131 |
|
|
boxy_num = boxy_old*dsign(1.0d0,ry(i))*int(abs(ry(i)/boxy_old)+0.5d0); |
132 |
|
|
boxz_num = boxz_old*dsign(1.0d0,rz(i))*int(abs(rz(i)/boxz_old)+0.5d0); |
133 |
|
|
|
134 |
|
|
rxi = rx(i) - boxx_num; |
135 |
|
|
ryi = ry(i) - boxy_num; |
136 |
|
|
rzi = rz(i) - boxz_num; |
137 |
|
|
|
138 |
|
|
// update the minimum image coordinates using the scaling factor |
139 |
|
|
rxi = rxi + rxi*percentScale; |
140 |
|
|
ryi = ryi + ryi*percentScale; |
141 |
|
|
rzi = rzi + rzi*percentScale; |
142 |
|
|
|
143 |
|
|
rx(i) = rxi + boxx_num; |
144 |
|
|
ry(i) = ryi + boxy_num; |
145 |
|
|
rz(i) = rzi + boxz_num; |
146 |
|
|
} |
147 |
|
|
} |