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colvargrid.cpp
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Created
Wed, Oct 2, 11:31
Size
3 KB
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text/x-c
Expires
Fri, Oct 4, 11:31 (2 d)
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blob
Format
Raw Data
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21280866
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rLAMMPS lammps
colvargrid.cpp
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// -*- c++ -*-
#include "colvarmodule.h"
#include "colvarvalue.h"
#include "colvarparse.h"
#include "colvar.h"
#include "colvarcomp.h"
#include "colvargrid.h"
colvar_grid_count
::
colvar_grid_count
()
:
colvar_grid
<
size_t
>
()
{
mult
=
1
;
}
colvar_grid_count
::
colvar_grid_count
(
std
::
vector
<
int
>
const
&
nx_i
,
size_t
const
&
def_count
)
:
colvar_grid
<
size_t
>
(
nx_i
,
def_count
,
1
)
{}
colvar_grid_count
::
colvar_grid_count
(
std
::
vector
<
colvar
*>
&
colvars
,
size_t
const
&
def_count
)
:
colvar_grid
<
size_t
>
(
colvars
,
def_count
,
1
)
{}
colvar_grid_scalar
::
colvar_grid_scalar
()
:
colvar_grid
<
cvm
::
real
>
(),
samples
(
NULL
),
grad
(
NULL
)
{}
colvar_grid_scalar
::
colvar_grid_scalar
(
colvar_grid_scalar
const
&
g
)
:
colvar_grid
<
cvm
::
real
>
(
g
),
samples
(
NULL
),
grad
(
NULL
)
{
grad
=
new
cvm
::
real
[
nd
];
}
colvar_grid_scalar
::
colvar_grid_scalar
(
std
::
vector
<
int
>
const
&
nx_i
)
:
colvar_grid
<
cvm
::
real
>
(
nx_i
,
0.0
,
1
),
samples
(
NULL
)
{
grad
=
new
cvm
::
real
[
nd
];
}
colvar_grid_scalar
::
colvar_grid_scalar
(
std
::
vector
<
colvar
*>
&
colvars
,
bool
margin
)
:
colvar_grid
<
cvm
::
real
>
(
colvars
,
0.0
,
1
,
margin
),
samples
(
NULL
)
{
grad
=
new
cvm
::
real
[
nd
];
}
colvar_grid_scalar
::~
colvar_grid_scalar
()
{
if
(
grad
)
{
delete
[]
grad
;
grad
=
NULL
;
}
}
cvm
::
real
colvar_grid_scalar
::
maximum_value
()
const
{
cvm
::
real
max
=
data
[
0
];
for
(
size_t
i
=
0
;
i
<
nt
;
i
++
)
{
if
(
data
[
i
]
>
max
)
max
=
data
[
i
];
}
return
max
;
}
cvm
::
real
colvar_grid_scalar
::
minimum_value
()
const
{
cvm
::
real
min
=
data
[
0
];
for
(
size_t
i
=
0
;
i
<
nt
;
i
++
)
{
if
(
data
[
i
]
<
min
)
min
=
data
[
i
];
}
return
min
;
}
cvm
::
real
colvar_grid_scalar
::
integral
()
const
{
cvm
::
real
sum
=
0.0
;
for
(
size_t
i
=
0
;
i
<
nt
;
i
++
)
{
sum
+=
data
[
i
];
}
cvm
::
real
bin_volume
=
1.0
;
for
(
size_t
id
=
0
;
id
<
widths
.
size
();
id
++
)
{
bin_volume
*=
widths
[
id
];
}
return
bin_volume
*
sum
;
}
cvm
::
real
colvar_grid_scalar
::
entropy
()
const
{
cvm
::
real
sum
=
0.0
;
for
(
size_t
i
=
0
;
i
<
nt
;
i
++
)
{
sum
+=
-
1.0
*
data
[
i
]
*
std
::
log
(
data
[
i
]);
}
cvm
::
real
bin_volume
=
1.0
;
for
(
size_t
id
=
0
;
id
<
widths
.
size
();
id
++
)
{
bin_volume
*=
widths
[
id
];
}
return
bin_volume
*
sum
;
}
colvar_grid_gradient
::
colvar_grid_gradient
()
:
colvar_grid
<
cvm
::
real
>
(),
samples
(
NULL
)
{}
colvar_grid_gradient
::
colvar_grid_gradient
(
std
::
vector
<
int
>
const
&
nx_i
)
:
colvar_grid
<
cvm
::
real
>
(
nx_i
,
0.0
,
nx_i
.
size
()),
samples
(
NULL
)
{}
colvar_grid_gradient
::
colvar_grid_gradient
(
std
::
vector
<
colvar
*>
&
colvars
)
:
colvar_grid
<
cvm
::
real
>
(
colvars
,
0.0
,
colvars
.
size
()),
samples
(
NULL
)
{}
void
colvar_grid_gradient
::
write_1D_integral
(
std
::
ostream
&
os
)
{
cvm
::
real
bin
,
min
,
integral
;
std
::
vector
<
cvm
::
real
>
int_vals
;
os
<<
"# xi A(xi)
\n
"
;
if
(
cv
.
size
()
!=
1
)
{
cvm
::
fatal_error
(
"Cannot write integral for multi-dimensional gradient grids."
);
}
integral
=
0.0
;
int_vals
.
push_back
(
0.0
);
min
=
0.0
;
// correction for periodic colvars, so that the PMF is periodic
cvm
::
real
corr
;
if
(
periodic
[
0
]
)
{
corr
=
average
();
}
else
{
corr
=
0.0
;
}
for
(
std
::
vector
<
int
>
ix
=
new_index
();
index_ok
(
ix
);
incr
(
ix
))
{
if
(
samples
)
{
size_t
const
samples_here
=
samples
->
value
(
ix
);
if
(
samples_here
)
integral
+=
(
value
(
ix
)
/
cvm
::
real
(
samples_here
)
-
corr
)
*
cv
[
0
]
->
width
;
}
else
{
integral
+=
(
value
(
ix
)
-
corr
)
*
cv
[
0
]
->
width
;
}
if
(
integral
<
min
)
min
=
integral
;
int_vals
.
push_back
(
integral
);
}
bin
=
0.0
;
for
(
int
i
=
0
;
i
<
nx
[
0
];
i
++
,
bin
+=
1.0
)
{
os
<<
std
::
setw
(
10
)
<<
cv
[
0
]
->
lower_boundary
.
real_value
+
cv
[
0
]
->
width
*
bin
<<
" "
<<
std
::
setw
(
cvm
::
cv_width
)
<<
std
::
setprecision
(
cvm
::
cv_prec
)
<<
int_vals
[
i
]
-
min
<<
"
\n
"
;
}
os
<<
std
::
setw
(
10
)
<<
cv
[
0
]
->
lower_boundary
.
real_value
+
cv
[
0
]
->
width
*
bin
<<
" "
<<
std
::
setw
(
cvm
::
cv_width
)
<<
std
::
setprecision
(
cvm
::
cv_prec
)
<<
int_vals
[
nx
[
0
]]
-
min
<<
"
\n
"
;
return
;
}
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