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rLAMMPS lammps
improper_cossq.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Georgios G. Vogiatzis (CoMSE, NTU Athens),
gvog@chemeng.ntua.gr
------------------------------------------------------------------------- */
#include <mpi.h>
#include <math.h>
#include <stdlib.h>
#include "improper_cossq.h"
#include "atom.h"
#include "comm.h"
#include "neighbor.h"
#include "domain.h"
#include "force.h"
#include "update.h"
#include "memory.h"
#include "error.h"
#include "math_const.h"
using
namespace
LAMMPS_NS
;
using
namespace
MathConst
;
#define TOLERANCE 0.05
#define SMALL 0.001
/* ---------------------------------------------------------------------- */
ImproperCossq
::
ImproperCossq
(
LAMMPS
*
lmp
)
:
Improper
(
lmp
)
{}
/* ---------------------------------------------------------------------- */
ImproperCossq
::~
ImproperCossq
()
{
if
(
allocated
)
{
memory
->
destroy
(
setflag
);
memory
->
destroy
(
k
);
memory
->
destroy
(
chi
);
}
}
/* ---------------------------------------------------------------------- */
void
ImproperCossq
::
compute
(
int
eflag
,
int
vflag
)
{
int
i1
,
i2
,
i3
,
i4
,
n
,
type
;
double
vb1x
,
vb1y
,
vb1z
,
vb2x
,
vb2y
,
vb2z
,
vb3x
,
vb3y
,
vb3z
;
double
eimproper
,
f1
[
3
],
f2
[
3
],
f3
[
3
],
f4
[
3
];
double
rjisq
,
rji
,
rlksq
,
rlk
,
cosphi
,
angfac
;
double
cjiji
,
clkji
,
clklk
,
cfact1
,
cfact2
,
cfact3
;
eimproper
=
0.0
;
if
(
eflag
||
vflag
)
ev_setup
(
eflag
,
vflag
);
else
evflag
=
0
;
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
int
**
improperlist
=
neighbor
->
improperlist
;
int
nimproperlist
=
neighbor
->
nimproperlist
;
int
nlocal
=
atom
->
nlocal
;
int
newton_bond
=
force
->
newton_bond
;
for
(
n
=
0
;
n
<
nimproperlist
;
n
++
)
{
/* Ask the improper list for the atom types. */
i1
=
improperlist
[
n
][
0
];
i2
=
improperlist
[
n
][
1
];
i3
=
improperlist
[
n
][
2
];
i4
=
improperlist
[
n
][
3
];
type
=
improperlist
[
n
][
4
];
/* separation vector between i1 and i2, (i2-i1) */
vb1x
=
x
[
i2
][
0
]
-
x
[
i1
][
0
];
vb1y
=
x
[
i2
][
1
]
-
x
[
i1
][
1
];
vb1z
=
x
[
i2
][
2
]
-
x
[
i1
][
2
];
rjisq
=
vb1x
*
vb1x
+
vb1y
*
vb1y
+
vb1z
*
vb1z
;
rji
=
sqrt
(
rjisq
);
/* separation vector between i2 and i3 (i3-i2) */
vb2x
=
x
[
i3
][
0
]
-
x
[
i2
][
0
];
vb2y
=
x
[
i3
][
1
]
-
x
[
i2
][
1
];
vb2z
=
x
[
i3
][
2
]
-
x
[
i2
][
2
];
/* separation vector between i3 and i4, (i4-i3) */
vb3x
=
x
[
i4
][
0
]
-
x
[
i3
][
0
];
vb3y
=
x
[
i4
][
1
]
-
x
[
i3
][
1
];
vb3z
=
x
[
i4
][
2
]
-
x
[
i3
][
2
];
rlksq
=
vb3x
*
vb3x
+
vb3y
*
vb3y
+
vb3z
*
vb3z
;
rlk
=
sqrt
(
rlksq
);
cosphi
=
(
vb3x
*
vb1x
+
vb3y
*
vb1y
+
vb3z
*
vb1z
)
/
(
rji
*
rlk
);
/* Check that cos(phi) is in the correct limits. */
if
(
cosphi
>
1.0
+
TOLERANCE
||
cosphi
<
(
-
1.0
-
TOLERANCE
))
{
int
me
;
MPI_Comm_rank
(
world
,
&
me
);
if
(
screen
)
{
char
str
[
128
];
sprintf
(
str
,
"Improper problem: %d "
BIGINT_FORMAT
" "
TAGINT_FORMAT
" "
TAGINT_FORMAT
" "
TAGINT_FORMAT
" "
TAGINT_FORMAT
,
me
,
update
->
ntimestep
,
atom
->
tag
[
i1
],
atom
->
tag
[
i2
],
atom
->
tag
[
i3
],
atom
->
tag
[
i4
]);
error
->
warning
(
FLERR
,
str
,
0
);
fprintf
(
screen
,
" 1st atom: %d %g %g %g
\n
"
,
me
,
x
[
i1
][
0
],
x
[
i1
][
1
],
x
[
i1
][
2
]);
fprintf
(
screen
,
" 2nd atom: %d %g %g %g
\n
"
,
me
,
x
[
i2
][
0
],
x
[
i2
][
1
],
x
[
i2
][
2
]);
fprintf
(
screen
,
" 3rd atom: %d %g %g %g
\n
"
,
me
,
x
[
i3
][
0
],
x
[
i3
][
1
],
x
[
i3
][
2
]);
fprintf
(
screen
,
" 4th atom: %d %g %g %g
\n
"
,
me
,
x
[
i4
][
0
],
x
[
i4
][
1
],
x
[
i4
][
2
]);
}
}
/* Apply corrections to round-off errors. */
if
(
cosphi
>
1.0
)
cosphi
-=
SMALL
;
if
(
cosphi
<
-
1.0
)
cosphi
+=
SMALL
;
/* Calculate the angle: */
double
torangle
=
acos
(
cosphi
);
cosphi
=
cos
(
torangle
-
chi
[
type
]);
if
(
eflag
)
eimproper
=
0.5
*
k
[
type
]
*
cosphi
*
cosphi
;
/*
printf("The tags: %d-%d-%d-%d, of type %d .\n",atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4],type);
printf("The ji vector: %f, %f, %f.\nThe lk vector: %f, %f, %f.\n", vb1x,vb1y,vb1z,vb3x,vb3y,vb3z);
printf("The cosine of the angle: %-1.16e.\n", cosphi);
printf("The energy of the improper: %-1.16e with prefactor %-1.16e.\n", eimproper, 0.5*k[type]);
*/
/* Work out forces. */
angfac
=
-
k
[
type
]
*
cosphi
;
cjiji
=
rjisq
;
clklk
=
rlksq
;
/*CLKJI = RXLK * RXJI + RYLK * RYJI + RZLK * RZJI */
clkji
=
vb3x
*
vb1x
+
vb3y
*
vb1y
+
vb3z
*
vb1z
;
/*CFACT1 = CLKLK * CJIJI
CFACT1 = SQRT(CFACT1)
CFACT1 = ANGFAC / CFACT1*/
cfact1
=
angfac
/
sqrt
(
clklk
*
cjiji
);
/*CFACT2 = CLKJI / CLKLK*/
cfact2
=
clkji
/
clklk
;
/*CFACT3 = CLKJI / CJIJI*/
cfact3
=
clkji
/
cjiji
;
/*FIX = -RXLK + CFACT3 * RXJI
FIY = -RYLK + CFACT3 * RYJI
FIZ = -RZLK + CFACT3 * RZJI*/
f1
[
0
]
=
-
vb3x
+
cfact3
*
vb1x
;
f1
[
1
]
=
-
vb3y
+
cfact3
*
vb1y
;
f1
[
2
]
=
-
vb3z
+
cfact3
*
vb1z
;
/*FJX = -FIX
FJY = -FIY
FJZ = -FIZ*/
f2
[
0
]
=
-
f1
[
0
];
f2
[
1
]
=
-
f1
[
1
];
f2
[
2
]
=
-
f1
[
2
];
/*FKX = CFACT2 * RXLK - RXJI
FKY = CFACT2 * RYLK - RYJI
FKZ = CFACT2 * RZLK - RZJI*/
f3
[
0
]
=
cfact2
*
vb3x
-
vb1x
;
f3
[
1
]
=
cfact2
*
vb3y
-
vb1y
;
f3
[
2
]
=
cfact2
*
vb3z
-
vb1z
;
/*FLX = -FKX
FLY = -FKY
FLZ = -FKZ*/
f4
[
0
]
=
-
f3
[
0
];
f4
[
1
]
=
-
f3
[
1
];
f4
[
2
]
=
-
f3
[
2
];
/*FIX = FIX * CFACT1
FIY = FIY * CFACT1
FIZ = FIZ * CFACT1*/
f1
[
0
]
*=
cfact1
;
f1
[
1
]
*=
cfact1
;
f1
[
2
]
*=
cfact1
;
/*FJX = FJX * CFACT1
FJY = FJY * CFACT1
FJZ = FJZ * CFACT1*/
f2
[
0
]
*=
cfact1
;
f2
[
1
]
*=
cfact1
;
f2
[
2
]
*=
cfact1
;
/*FKX = FKX * CFACT1
FKY = FKY * CFACT1
FKZ = FKZ * CFACT1*/
f3
[
0
]
*=
cfact1
;
f3
[
1
]
*=
cfact1
;
f3
[
2
]
*=
cfact1
;
/*FLX = FLX * CFACT1
FLY = FLY * CFACT1
FLZ = FLZ * CFACT1*/
f4
[
0
]
*=
cfact1
;
f4
[
1
]
*=
cfact1
;
f4
[
2
]
*=
cfact1
;
/* Apply force to each of 4 atoms */
if
(
newton_bond
||
i1
<
nlocal
)
{
f
[
i1
][
0
]
+=
f1
[
0
];
f
[
i1
][
1
]
+=
f1
[
1
];
f
[
i1
][
2
]
+=
f1
[
2
];
}
if
(
newton_bond
||
i2
<
nlocal
)
{
f
[
i2
][
0
]
+=
f2
[
0
];
f
[
i2
][
1
]
+=
f2
[
1
];
f
[
i2
][
2
]
+=
f2
[
2
];
}
if
(
newton_bond
||
i3
<
nlocal
)
{
f
[
i3
][
0
]
+=
f3
[
0
];
f
[
i3
][
1
]
+=
f3
[
1
];
f
[
i3
][
2
]
+=
f3
[
2
];
}
if
(
newton_bond
||
i4
<
nlocal
)
{
f
[
i4
][
0
]
+=
f4
[
0
];
f
[
i4
][
1
]
+=
f4
[
1
];
f
[
i4
][
2
]
+=
f4
[
2
];
}
if
(
evflag
)
ev_tally
(
i1
,
i2
,
i3
,
i4
,
nlocal
,
newton_bond
,
eimproper
,
f1
,
f3
,
f4
,
-
vb1x
,
-
vb1y
,
-
vb1z
,
vb2x
,
vb2y
,
vb2z
,
vb3x
,
vb3y
,
vb3z
);
}
}
/* ---------------------------------------------------------------------- */
void
ImproperCossq
::
allocate
()
{
allocated
=
1
;
int
n
=
atom
->
nimpropertypes
;
memory
->
create
(
k
,
n
+
1
,
"improper:k"
);
memory
->
create
(
chi
,
n
+
1
,
"improper:chi"
);
memory
->
create
(
setflag
,
n
+
1
,
"improper:setflag"
);
for
(
int
i
=
1
;
i
<=
n
;
i
++
)
setflag
[
i
]
=
0
;
}
/* ----------------------------------------------------------------------
set coeffs for one type
------------------------------------------------------------------------- */
void
ImproperCossq
::
coeff
(
int
narg
,
char
**
arg
)
{
/* Check whether there exist sufficient number of arguments.
0: type of improper to be applied to
1: energetic constant
2: equilibrium angle in degrees */
if
(
narg
!=
3
)
error
->
all
(
FLERR
,
"Incorrect args for cossq improper coefficients"
);
if
(
!
allocated
)
allocate
();
int
ilo
,
ihi
;
force
->
bounds
(
arg
[
0
],
atom
->
nimpropertypes
,
ilo
,
ihi
);
double
k_one
=
force
->
numeric
(
FLERR
,
arg
[
1
]);
double
chi_one
=
force
->
numeric
(
FLERR
,
arg
[
2
]);
int
count
=
0
;
for
(
int
i
=
ilo
;
i
<=
ihi
;
i
++
)
{
k
[
i
]
=
k_one
;
chi
[
i
]
=
((
chi_one
*
MY_PI
)
/
180.0
);
setflag
[
i
]
=
1
;
count
++
;
}
if
(
count
==
0
)
error
->
all
(
FLERR
,
"Incorrect args for improper coefficients"
);
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void
ImproperCossq
::
write_restart
(
FILE
*
fp
)
{
fwrite
(
&
k
[
1
],
sizeof
(
double
),
atom
->
nimpropertypes
,
fp
);
fwrite
(
&
chi
[
1
],
sizeof
(
double
),
atom
->
nimpropertypes
,
fp
);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void
ImproperCossq
::
read_restart
(
FILE
*
fp
)
{
allocate
();
if
(
comm
->
me
==
0
)
{
fread
(
&
k
[
1
],
sizeof
(
double
),
atom
->
nimpropertypes
,
fp
);
fread
(
&
chi
[
1
],
sizeof
(
double
),
atom
->
nimpropertypes
,
fp
);
}
MPI_Bcast
(
&
k
[
1
],
atom
->
nimpropertypes
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
chi
[
1
],
atom
->
nimpropertypes
,
MPI_DOUBLE
,
0
,
world
);
for
(
int
i
=
1
;
i
<=
atom
->
nimpropertypes
;
i
++
)
setflag
[
i
]
=
1
;
}
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