forked from Allen-Tildesley/examples
-
Notifications
You must be signed in to change notification settings - Fork 0
/
md_lj_le_module.f90
194 lines (151 loc) · 8.24 KB
/
md_lj_le_module.f90
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
! md_lj_le_module.f90
! Force routine for MD, LJ atoms, Lees-Edwards boundaries
MODULE md_module
!------------------------------------------------------------------------------------------------!
! This software was written in 2016/17 !
! by Michael P. Allen <m.p.allen@warwick.ac.uk>/<m.p.allen@bristol.ac.uk> !
! and Dominic J. Tildesley <d.tildesley7@gmail.com> ("the authors"), !
! to accompany the book "Computer Simulation of Liquids", second edition, 2017 ("the text"), !
! published by Oxford University Press ("the publishers"). !
! !
! LICENCE !
! Creative Commons CC0 Public Domain Dedication. !
! To the extent possible under law, the authors have dedicated all copyright and related !
! and neighboring rights to this software to the PUBLIC domain worldwide. !
! This software is distributed without any warranty. !
! You should have received a copy of the CC0 Public Domain Dedication along with this software. !
! If not, see <http://creativecommons.org/publicdomain/zero/1.0/>. !
! !
! DISCLAIMER !
! The authors and publishers make no warranties about the software, and disclaim liability !
! for all uses of the software, to the fullest extent permitted by applicable law. !
! The authors and publishers do not recommend use of this software for any purpose. !
! It is made freely available, solely to clarify points made in the text. When using or citing !
! the software, you should not imply endorsement by the authors or publishers. !
!------------------------------------------------------------------------------------------------!
USE, INTRINSIC :: iso_fortran_env, ONLY : output_unit, error_unit
IMPLICIT NONE
PRIVATE
! Public routines
PUBLIC :: introduction, conclusion, allocate_arrays, deallocate_arrays
PUBLIC :: force
! Public data
INTEGER, PUBLIC :: n ! Number of atoms
REAL, DIMENSION(:,:), ALLOCATABLE, PUBLIC :: r ! Positions (3,n)
REAL, DIMENSION(:,:), ALLOCATABLE, PUBLIC :: v ! Velocities (3,n)
REAL, DIMENSION(:,:), ALLOCATABLE, PUBLIC :: f ! Forces (3,n)
! Private data
REAL, PARAMETER :: r_cut_sq = 2.0**(1.0/3.0), r_cut = SQRT(r_cut_sq) ! Minimum and cutoff of WCA LJ potential
! Public derived type
TYPE, PUBLIC :: potential_type ! A composite variable for interactions comprising
REAL :: pot ! the potential energy
REAL :: vir ! the virial and
REAL :: lap ! the Laplacian and
REAL :: pyx ! the off-diagonal virial part of the pressure tensor
LOGICAL :: ovr ! a flag indicating overlap (i.e. pot too high to use)
CONTAINS
PROCEDURE :: add_potential_type
GENERIC :: OPERATOR(+) => add_potential_type
END TYPE potential_type
CONTAINS
FUNCTION add_potential_type ( a, b ) RESULT (c)
IMPLICIT NONE
TYPE(potential_type) :: c ! Result is the sum of
CLASS(potential_type), INTENT(in) :: a, b ! the two inputs
c%pot = a%pot + b%pot
c%vir = a%vir + b%vir
c%pyx = a%pyx + b%pyx
c%lap = a%lap + b%lap
c%ovr = a%ovr .OR. b%ovr
END FUNCTION add_potential_type
SUBROUTINE introduction
IMPLICIT NONE
WRITE ( unit=output_unit, fmt='(a)' ) 'WCA shifted Lennard-Jones potential'
WRITE ( unit=output_unit, fmt='(a)' ) 'Diameter, sigma = 1'
WRITE ( unit=output_unit, fmt='(a)' ) 'Well depth, epsilon = 1'
WRITE ( unit=output_unit, fmt='(a)' ) 'Lees-Edwards boundaries'
END SUBROUTINE introduction
SUBROUTINE conclusion
IMPLICIT NONE
WRITE ( unit=output_unit, fmt='(a)') 'Program ends'
END SUBROUTINE conclusion
SUBROUTINE allocate_arrays ( box )
IMPLICIT NONE
REAL, INTENT(in) :: box ! Simulation box length
REAL :: r_cut_box
ALLOCATE ( r(3,n), v(3,n), f(3,n) )
r_cut_box = r_cut / box
IF ( r_cut_box > 0.5 ) THEN
WRITE ( unit=error_unit, fmt='(a,f15.6)' ) 'r_cut/box too large ', r_cut_box
STOP 'Error in allocate_arrays'
END IF
END SUBROUTINE allocate_arrays
SUBROUTINE deallocate_arrays
IMPLICIT NONE
DEALLOCATE ( r, v, f )
END SUBROUTINE deallocate_arrays
SUBROUTINE force ( box, strain, total )
IMPLICIT NONE
REAL, INTENT(in) :: box ! Simulation box length
REAL, INTENT(in) :: strain ! Shear strain
TYPE(potential_type), INTENT(out) :: total ! Composite of pot, vir, lap etc
! total%pot is the WCA LJ potential energy for whole system
! total%vir is the corresponding virial
! total%pyx is the virial part of the yx-element of the pressure tensor
! total%lap is the corresponding Laplacian
! total%ovr is a warning flag that there is an overlap
! This routine also calculates forces and stores them in the array f
! If total%ovr is set to .true., the forces etc should not be used
! It is assumed that positions are in units where box = 1
! Forces are calculated in units where sigma = 1 and epsilon = 1
! Lees-Edwards boundaries, in sliding brick arrangement
! Flow/gradient/vorticity directions are x/y/z == 1/2/3
INTEGER :: i, j
REAL :: r_cut_box, r_cut_box_sq, box_sq, rij_sq
REAL :: sr2, sr6, sr12
REAL, DIMENSION(3) :: rij, fij
REAL, PARAMETER :: sr2_ovr = 1.77 ! overlap threshold (pot > 100)
TYPE(potential_type) :: pair
r_cut_box = r_cut / box
r_cut_box_sq = r_cut_box ** 2
box_sq = box ** 2
IF ( r_cut_box > 0.5 ) THEN
WRITE ( unit=error_unit, fmt='(a,f15.6)' ) 'r_cut/box too large ', r_cut_box
STOP 'Error in force'
END IF
! Initialize
f = 0.0
total = potential_type ( pot=0.0, vir=0.0, pyx=0.0, lap=0.0, ovr=.FALSE. )
DO i = 1, n - 1 ! Begin outer loop over atoms
DO j = i + 1, n ! Begin inner loop over atoms
rij(:) = r(:,i) - r(:,j) ! Separation vector
rij(1) = rij(1) - ANINT ( rij(2) ) * strain ! Extra correction in box=1 units
rij(:) = rij(:) - ANINT ( rij(:) ) ! Periodic boundary conditions in box=1 units
rij_sq = SUM ( rij**2 ) ! Squared separation
IF ( rij_sq < r_cut_box_sq ) THEN ! Check within cutoff
rij_sq = rij_sq * box_sq ! Now in sigma=1 units
rij(:) = rij(:) * box ! Now in sigma=1 units
sr2 = 1.0 / rij_sq ! (sigma/rij)**2
pair%ovr = sr2 > sr2_ovr ! Overlap if too close
sr6 = sr2 ** 3
sr12 = sr6 ** 2
pair%pot = sr12 - sr6 ! LJ pair potential (cut but not shifted)
pair%vir = pair%pot + sr12 ! LJ pair virial
pair%pot = pair%pot + 0.25 ! WCA LJ pair potential (cut-and-shifted)
pair%lap = ( 22.0*sr12 - 5.0*sr6 ) * sr2 ! LJ pair Laplacian
fij = rij * pair%vir * sr2 ! LJ pair forces
pair%pyx = rij(2)*fij(1) ! Off-diagonal element of pressure tensor
total = total + pair
f(:,i) = f(:,i) + fij
f(:,j) = f(:,j) - fij
END IF ! End check within cutoff
END DO ! End inner loop over atoms
END DO ! End outer loop over atoms
! Multiply results by numerical factors
f = f * 24.0 ! 24*epsilon
total%pot = total%pot * 4.0 ! 4*epsilon
total%vir = total%vir * 24.0 / 3.0 ! 24*epsilon and divide virial by 3
total%pyx = total%pyx * 24.0 ! 24*epsilon
total%lap = total%lap * 24.0 * 2.0 ! 24*epsilon and factor 2 for ij and ji
END SUBROUTINE force
END MODULE md_module