| 1 |
!=========================================================================== |
| 2 |
! |
| 3 |
!=========================================================================== |
| 4 |
! . Subroutines: |
| 5 |
! LANGEVIN_VERLET_DYNAMICS molecular dynamics using langevin |
| 6 |
! dynamics |
| 7 |
!=========================================================================== |
| 8 |
|
| 9 |
|
| 10 |
module dynamics_langevin_verlet |
| 11 |
use definitions, ONLY : DP,NDIM |
| 12 |
use constants, ONLY : AMU_TO_KG,K_BOLTZ,MS_TO_AFS, & |
| 13 |
KCALMOL_TO_AMUA2FS2, PI |
| 14 |
use simulation |
| 15 |
use parameter |
| 16 |
use force_module, ONLY : calc_forces |
| 17 |
use second_deriv |
| 18 |
use force_utilities, ONLY : check |
| 19 |
use status |
| 20 |
! use velocity, ONLY : scale_velocities |
| 21 |
use dynamics_utilities, ONLY : evolve_time, init_dynamics_loop, & |
| 22 |
sim_status,DT2,DTSQRT,DTSQ2, init_status |
| 23 |
use velocity, ONLY : calc_temp |
| 24 |
#ifdef MPI |
| 25 |
use mpi_module, ONLY : mpi_comm_world,mpi_err |
| 26 |
#endif |
| 27 |
|
| 28 |
implicit none |
| 29 |
PRIVATE |
| 30 |
SAVE |
| 31 |
|
| 32 |
! . Constants common to langevin dynamcics |
| 33 |
|
| 34 |
real ( kind = dp ) :: C0,C1,C2 |
| 35 |
real ( kind = dp ), allocatable, dimension(:) :: CRV1,CRV2 |
| 36 |
real ( kind = dp ), allocatable, dimension(:) :: FACR1,FACR2 |
| 37 |
real ( kind = dp ), allocatable, dimension(:) :: FACV1,FACV2,FACV3 |
| 38 |
|
| 39 |
real ( kind = dp ), allocatable, dimension(:) :: SDR,SDV |
| 40 |
|
| 41 |
|
| 42 |
! . langevin arrays |
| 43 |
real ( kind = dp ), allocatable, dimension(:,:) :: v_lang |
| 44 |
real ( kind = dp ), allocatable, dimension(:) :: MASFAC |
| 45 |
|
| 46 |
type (sim_status) :: langevin_status |
| 47 |
|
| 48 |
public :: langevin_verlet_dynamics |
| 49 |
|
| 50 |
|
| 51 |
|
| 52 |
|
| 53 |
contains |
| 54 |
|
| 55 |
! . subroutine init_langevin sets up common |
| 56 |
! constants for dynamics |
| 57 |
subroutine init_langevin |
| 58 |
use model_module, ONLY : get_max_atype |
| 59 |
integer :: n_atypes_known |
| 60 |
character(len=80) :: msg |
| 61 |
real( kind = dp ) :: fact |
| 62 |
real( kind = dp ) :: this_eta |
| 63 |
! . allocate nlocal arrays |
| 64 |
allocate(v_lang(ndim,nlocal)) |
| 65 |
allocate(masfac(nlocal)) |
| 66 |
! . find out how many atypes the simulation |
| 67 |
! . knows about |
| 68 |
|
| 69 |
n_atypes_known = get_max_atype() |
| 70 |
allocate(SDR(n_atypes_known)) |
| 71 |
allocate(SDV(n_atypes_known)) |
| 72 |
allocate(CRV1(n_atypes_known)) |
| 73 |
allocate(CRV2(n_atypes_known)) |
| 74 |
allocate(FACR1(n_atypes_known)) |
| 75 |
allocate(FACR2(n_atypes_known)) |
| 76 |
allocate(FACV1(n_atypes_known)) |
| 77 |
allocate(FACV2(n_atypes_known)) |
| 78 |
allocate(FACV3(n_atypes_known)) |
| 79 |
|
| 80 |
|
| 81 |
this_eta = eta |
| 82 |
call calc_gamma_factors(this_eta) |
| 83 |
|
| 84 |
! . Temperature and mass factors. |
| 85 |
FACT = ( K_BOLTZ * bath_temp / AMU_TO_KG ) |
| 86 |
!!!!!DANGER DANGER WILL |
| 87 |
! WHERE ( .NOT. ATMFIX ) MASFAC = MS_TO_AFS * SQRT ( FACT / mass ) ! A fs^-1. |
| 88 |
MASFAC = MS_TO_AFS * SQRT ( FACT / mass ) ! A fs^-1. |
| 89 |
|
| 90 |
write(msg,*) "Visocity of solvent is: ", eta |
| 91 |
call info("INIT_LANGEVIN",msg) |
| 92 |
|
| 93 |
|
| 94 |
end subroutine init_langevin |
| 95 |
|
| 96 |
|
| 97 |
subroutine langevin_verlet_dynamics() |
| 98 |
use langevin_cluster_list, ONLY : init_langevin_list,create_langevin_list |
| 99 |
|
| 100 |
|
| 101 |
logical :: update_nlist |
| 102 |
logical :: do_pot |
| 103 |
logical :: not_done |
| 104 |
logical :: nmflag |
| 105 |
|
| 106 |
integer :: step, i |
| 107 |
real(kind = dp) :: temp |
| 108 |
call init_status(langevin_status) |
| 109 |
call init_dynamics_loop(langevin_status) |
| 110 |
call init_langevin_list(nlocal) |
| 111 |
! Start the main simulation loop. |
| 112 |
|
| 113 |
do_pot = .true. |
| 114 |
not_done = .true. |
| 115 |
nmflag = .false. |
| 116 |
step = 0 |
| 117 |
!. initialize constants for dynamics |
| 118 |
call init_langevin() |
| 119 |
call create_langevin_list() |
| 120 |
dynamics: do |
| 121 |
if (.not.not_done) exit dynamics |
| 122 |
|
| 123 |
step = step + 1 |
| 124 |
|
| 125 |
|
| 126 |
! if (checktemp.and.(mod(step,check_temp_steps).eq.0)) then |
| 127 |
! call calc_temp(langevin_status%temp) |
| 128 |
! if (dabs(langevin_status%temp-target_temp).gt.therm_variance) then |
| 129 |
! call scale_velocities(target_temp) |
| 130 |
! end if |
| 131 |
! end if |
| 132 |
|
| 133 |
|
| 134 |
|
| 135 |
call check(update_nlist) |
| 136 |
if (update_nlist) then |
| 137 |
call create_langevin_list() |
| 138 |
endif |
| 139 |
|
| 140 |
call langevina() |
| 141 |
|
| 142 |
! . Add in random forces |
| 143 |
call RANDOM_FORCES |
| 144 |
|
| 145 |
if (do_pot) then |
| 146 |
call calc_forces(update_nlist,nmflag,pe = langevin_status%pot_e) |
| 147 |
else |
| 148 |
call calc_forces(update_nlist,nmflag) |
| 149 |
endif |
| 150 |
|
| 151 |
|
| 152 |
call langevinb() |
| 153 |
|
| 154 |
call evolve_time(step,langevin_status,do_pot,not_done) |
| 155 |
|
| 156 |
|
| 157 |
#ifdef MPI |
| 158 |
call mpi_barrier(mpi_comm_world,mpi_err) |
| 159 |
#endif |
| 160 |
end do dynamics |
| 161 |
|
| 162 |
deallocate(v_lang) |
| 163 |
deallocate(masfac) |
| 164 |
end subroutine langevin_verlet_dynamics |
| 165 |
|
| 166 |
|
| 167 |
! . First part of langevin dynamics |
| 168 |
! Advances positions from T to T + DT |
| 169 |
! Advances velocities from T to T + DT/2 |
| 170 |
!=================================== |
| 171 |
subroutine langevina() |
| 172 |
!=================================== |
| 173 |
use langevin_cluster_list, ONLY : langevin_list |
| 174 |
integer :: i |
| 175 |
! units for time are femtosec (10^-15 sec) |
| 176 |
! units for distance are angstroms (10^-10 m) |
| 177 |
! units for velocity are angstroms femtosec^-1 |
| 178 |
! units for mass are a.m.u. (1.661 * 10^-27 kg) |
| 179 |
! units for force are kcal mol^-1 angstrom^-1 |
| 180 |
! |
| 181 |
! converter will put the final terms into angstroms. |
| 182 |
! or angstrom/femtosecond. |
| 183 |
|
| 184 |
! Calculate new positions and velocities |
| 185 |
v_lang = 0.0_DP |
| 186 |
|
| 187 |
do i = 1, nlocal |
| 188 |
if (langevin_list(i)) then |
| 189 |
|
| 190 |
q(1:ndim,i) = q(1:ndim,i) + & |
| 191 |
FACR1(ident(i)) * v(1:ndim,i) + & |
| 192 |
(FACR2(ident(i)) * f(1:ndim,i)/mass(i))*KCALMOL_TO_AMUA2FS2 |
| 193 |
v_lang(1:ndim,i) = FACV1(ident(i)) * v(1:ndim,i) + & |
| 194 |
(FACV2(ident(i)) * f(1:ndim,i)/mass(i)) * KCALMOL_TO_AMUA2FS2 |
| 195 |
|
| 196 |
else |
| 197 |
q(1:ndim,i) = q(1:ndim,i) + dt*v(1:ndim,i) & |
| 198 |
+ (dtsq2*f(1:ndim,i)/mass(i))*KCALMOL_TO_AMUA2FS2 |
| 199 |
v(1:ndim,i) = v(1:ndim,i) & |
| 200 |
+ (dt2*f(1:ndim,i)/mass(i))*KCALMOL_TO_AMUA2FS2 |
| 201 |
|
| 202 |
endif |
| 203 |
|
| 204 |
|
| 205 |
end do |
| 206 |
|
| 207 |
end subroutine langevina |
| 208 |
|
| 209 |
|
| 210 |
!======================== |
| 211 |
subroutine langevinb( ) |
| 212 |
!========================= |
| 213 |
use langevin_cluster_list, ONLY : langevin_list |
| 214 |
integer :: i |
| 215 |
! units for time are femtosec (10^-15 sec) |
| 216 |
! units for distance are angstroms (10^-10 m) |
| 217 |
! units for velocity are angstroms femtosec^-1 |
| 218 |
! units for mass are a.m.u. (1.661 * 10^-27 kg) |
| 219 |
! units for force are kcal mol^-1 angstrom^-1 |
| 220 |
|
| 221 |
do i = 1, nlocal |
| 222 |
if (langevin_list(i)) then |
| 223 |
v(1:ndim,i) = v_lang(1:ndim,i) & |
| 224 |
+ (FACV3(ident(i)) * f(1:ndim,i)/mass(i))*KCALMOL_TO_AMUA2FS2 |
| 225 |
else ! standard movea |
| 226 |
v(1:ndim,i) = v(1:ndim,i) & |
| 227 |
+ (dt2*f(1:ndim,i)/mass(i))*KCALMOL_TO_AMUA2FS2 |
| 228 |
endif |
| 229 |
enddo |
| 230 |
|
| 231 |
end subroutine langevinb |
| 232 |
|
| 233 |
|
| 234 |
|
| 235 |
!----------------------- |
| 236 |
SUBROUTINE RANDOM_FORCES |
| 237 |
!----------------------- |
| 238 |
use langevin_cluster_list, ONLY : langevin_list |
| 239 |
use sprng_mod, ONLY : random_gauss |
| 240 |
! . Local scalars. |
| 241 |
INTEGER :: I, IATOM |
| 242 |
REAL ( KIND = DP ) :: RANR, RANV, R1, R2 |
| 243 |
|
| 244 |
! . Loop over the atoms. |
| 245 |
DO IATOM = 1,nlocal |
| 246 |
|
| 247 |
! . The atom is free. |
| 248 |
IF ( langevin_list(iatom) ) THEN |
| 249 |
|
| 250 |
! . Loop over the Cartesian components for the atom. |
| 251 |
DO I = 1,ndim |
| 252 |
|
| 253 |
! . Generate two Gaussian random numbers. |
| 254 |
R1 = RANDOM_GAUSS ( ) |
| 255 |
R2 = RANDOM_GAUSS ( ) |
| 256 |
|
| 257 |
! . Calculate the position and velocity changes. |
| 258 |
RANR = MASFAC(IATOM) * SDR(ident(iatom)) * R1 |
| 259 |
RANV = MASFAC(IATOM) * SDV(ident(iatom)) * & |
| 260 |
( CRV1(ident(iatom)) * R1 + CRV2(ident(iatom)) * R2 ) |
| 261 |
|
| 262 |
! . Add in the components. |
| 263 |
q(I,IATOM) = q(I,IATOM) + RANR |
| 264 |
v_lang(I,IATOM) = v_lang(I,IATOM) + RANV |
| 265 |
|
| 266 |
END DO |
| 267 |
END IF |
| 268 |
END DO |
| 269 |
|
| 270 |
END SUBROUTINE RANDOM_FORCES |
| 271 |
|
| 272 |
SUBROUTINE calc_gamma_factors(this_eta) |
| 273 |
use model_module, ONLY : atype_mass,atype_identifier |
| 274 |
integer :: atype, i |
| 275 |
character(len = 80) :: msg |
| 276 |
real( kind = dp ), intent(in) :: this_eta |
| 277 |
real( kind = dp ) :: gamma |
| 278 |
real( kind = dp ) :: FACT |
| 279 |
real( kind = dp ) :: C0 |
| 280 |
real( kind = dp ) :: C1 |
| 281 |
real( kind = dp ) :: C2 |
| 282 |
|
| 283 |
|
| 284 |
do i = 1, n_atypes_present |
| 285 |
gamma = 0.0_DP |
| 286 |
fact = 0.0_DP |
| 287 |
C0 = 0.0_DP |
| 288 |
C1 = 0.0_DP |
| 289 |
C2 = 0.0_DP |
| 290 |
|
| 291 |
atype = present_atypes(i) |
| 292 |
!. calculate Gamma in fs^-1 |
| 293 |
!. gamma = (6 * pi * atom sigma(angstroms) * viscosity(poise) * 100cm/m) * 1fs/10^-15sec / |
| 294 |
!. (atom mass(amu) * amu_to_kg * 1000g/kg) |
| 295 |
|
| 296 |
gamma = (6 * pi * get_langevin_sigma(atype) * this_eta ) / & |
| 297 |
(atype_mass(atype)*amu_to_kg*10) * 1E-15_DP |
| 298 |
write(msg,*) "Gamma for ",atype_identifier(atype), "is: ", gamma |
| 299 |
call info("CALC_GAMMA_FACTORS",msg) |
| 300 |
|
| 301 |
FACT = dt * gamma |
| 302 |
|
| 303 |
C0 = EXP ( - FACT ) |
| 304 |
C1 = ( 1.0_DP - C0 ) / FACT |
| 305 |
C2 = ( 1.0_DP - C1 ) / FACT |
| 306 |
|
| 307 |
! . Random force constants. |
| 308 |
SDR(atype) = SQRT ( dt * dt * & |
| 309 |
( 2.0_DP - ( 3.0_DP - 4.0_DP * C0 + C0 * C0 ) / FACT ) / FACT ) ! fs. |
| 310 |
SDV(atype) = SQRT ( ( 1.0_DP - C0 * C0 ) ) ! Dimensionless. |
| 311 |
CRV1(atype) = dt * ( 1.0_DP - C0 )**2 / ( FACT * SDR(atype) * SDV(atype) ) ! Dimensionless. |
| 312 |
CRV2(atype) = SQRT ( 1.0_DP - CRV1(atype) * CRV1(atype) ) ! Dimensionless. |
| 313 |
|
| 314 |
|
| 315 |
! . Calculate some integration constants. |
| 316 |
FACR1(atype) = C1 * dt ! fs. |
| 317 |
FACR2(atype) = C2 * dt * dt ! fs^2. |
| 318 |
FACV1(atype) = C0 ! Dimensionless. |
| 319 |
FACV2(atype) = ( C1 - C2 ) * dt ! fs. |
| 320 |
FACV3(atype) = C2 * dt ! fs. |
| 321 |
|
| 322 |
end do |
| 323 |
END SUBROUTINE calc_gamma_factors |
| 324 |
|
| 325 |
|
| 326 |
function get_langevin_sigma(this_atype) result(this_sigma) |
| 327 |
integer, intent(in) :: this_atype |
| 328 |
real( kind = dp ) :: this_sigma |
| 329 |
include 'headers/atom.h' |
| 330 |
|
| 331 |
select case (this_atype) |
| 332 |
|
| 333 |
case(Au_atom) |
| 334 |
this_sigma = 1.647E-10_DP |
| 335 |
case(Ag_atom) |
| 336 |
this_sigma = 1.574E-10_DP |
| 337 |
case(Pt_atom) |
| 338 |
this_sigma = 1.377E-10_DP |
| 339 |
case(Pb_atom) |
| 340 |
this_sigma = 2.148E-10_DP |
| 341 |
case(Cu_atom) |
| 342 |
this_sigma = 1.748E-10_DP |
| 343 |
case(Ni_atom) |
| 344 |
this_sigma = 1.417E-10_DP |
| 345 |
case(Pd_atom) |
| 346 |
this_sigma = 1.450E-10_DP |
| 347 |
case default |
| 348 |
call error("get_langevin_sigma","Unknown atom type") |
| 349 |
end select |
| 350 |
end function get_langevin_sigma |
| 351 |
end module dynamics_langevin_verlet |
