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colvarbias.cpp
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Wed, Sep 4, 04:28
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5 KB
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text/x-c
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Fri, Sep 6, 04:28 (2 d)
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blob
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20516166
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rLAMMPS lammps
colvarbias.cpp
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// -*- c++ -*-
#include "colvarmodule.h"
#include "colvarvalue.h"
#include "colvarbias.h"
colvarbias
::
colvarbias
(
char
const
*
key
)
:
bias_type
(
to_lower_cppstr
(
key
))
{
init_cvb_requires
();
rank
=
1
;
if
(
bias_type
==
std
::
string
(
"abf"
))
{
rank
=
cvm
::
n_abf_biases
+
1
;
}
if
(
bias_type
==
std
::
string
(
"harmonic"
)
||
bias_type
==
std
::
string
(
"linear"
))
{
rank
=
cvm
::
n_rest_biases
+
1
;
}
if
(
bias_type
==
std
::
string
(
"histogram"
))
{
rank
=
cvm
::
n_histo_biases
+
1
;
}
if
(
bias_type
==
std
::
string
(
"metadynamics"
))
{
rank
=
cvm
::
n_meta_biases
+
1
;
}
has_data
=
false
;
b_output_energy
=
false
;
reset
();
// Start in active state by default
enable
(
f_cvb_active
);
}
int
colvarbias
::
init
(
std
::
string
const
&
conf
)
{
colvarparse
::
init
(
conf
);
if
(
name
.
size
()
==
0
)
{
cvm
::
log
(
"Initializing a new
\"
"
+
bias_type
+
"
\"
instance.
\n
"
);
get_keyval
(
conf
,
"name"
,
name
,
bias_type
+
cvm
::
to_str
(
rank
));
{
colvarbias
*
bias_with_name
=
cvm
::
bias_by_name
(
this
->
name
);
if
(
bias_with_name
!=
NULL
)
{
if
((
bias_with_name
->
rank
!=
this
->
rank
)
||
(
bias_with_name
->
bias_type
!=
this
->
bias_type
))
{
cvm
::
error
(
"Error: this bias cannot have the same name,
\"
"
+
this
->
name
+
"
\"
, as another bias.
\n
"
,
INPUT_ERROR
);
return
INPUT_ERROR
;
}
}
}
description
=
"bias "
+
name
;
{
// lookup the associated colvars
std
::
vector
<
std
::
string
>
colvar_names
;
if
(
get_keyval
(
conf
,
"colvars"
,
colvar_names
))
{
if
(
colvars
.
size
())
{
cvm
::
error
(
"Error: cannot redefine the colvars that a bias was already defined on.
\n
"
,
INPUT_ERROR
);
return
INPUT_ERROR
;
}
for
(
size_t
i
=
0
;
i
<
colvar_names
.
size
();
i
++
)
{
add_colvar
(
colvar_names
[
i
]);
}
}
}
if
(
!
colvars
.
size
())
{
cvm
::
error
(
"Error: no collective variables specified.
\n
"
,
INPUT_ERROR
);
return
INPUT_ERROR
;
}
}
else
{
cvm
::
log
(
"Reinitializing bias
\"
"
+
name
+
"
\"
.
\n
"
);
}
get_keyval
(
conf
,
"outputEnergy"
,
b_output_energy
,
b_output_energy
);
return
COLVARS_OK
;
}
int
colvarbias
::
reset
()
{
bias_energy
=
0.0
;
for
(
size_t
i
=
0
;
i
<
colvars
.
size
();
i
++
)
{
colvar_forces
[
i
].
reset
();
}
return
COLVARS_OK
;
}
colvarbias
::
colvarbias
()
:
colvarparse
(),
has_data
(
false
)
{}
colvarbias
::~
colvarbias
()
{
colvarbias
::
clear
();
}
int
colvarbias
::
clear
()
{
// Remove references to this bias from colvars
for
(
std
::
vector
<
colvar
*>::
iterator
cvi
=
colvars
.
begin
();
cvi
!=
colvars
.
end
();
++
cvi
)
{
for
(
std
::
vector
<
colvarbias
*>::
iterator
bi
=
(
*
cvi
)
->
biases
.
begin
();
bi
!=
(
*
cvi
)
->
biases
.
end
();
++
bi
)
{
if
(
*
bi
==
this
)
{
(
*
cvi
)
->
biases
.
erase
(
bi
);
break
;
}
}
}
// ...and from the colvars module
for
(
std
::
vector
<
colvarbias
*>::
iterator
bi
=
cvm
::
biases
.
begin
();
bi
!=
cvm
::
biases
.
end
();
++
bi
)
{
if
(
*
bi
==
this
)
{
cvm
::
biases
.
erase
(
bi
);
break
;
}
}
return
COLVARS_OK
;
}
int
colvarbias
::
add_colvar
(
std
::
string
const
&
cv_name
)
{
if
(
colvar
*
cv
=
cvm
::
colvar_by_name
(
cv_name
))
{
// Removed this as nor all biases apply forces eg histogram
// cv->enable(colvar::task_gradients);
if
(
cvm
::
debug
())
{
cvm
::
log
(
"Applying this bias to collective variable
\"
"
+
cv
->
name
+
"
\"
.
\n
"
);
}
colvars
.
push_back
(
cv
);
colvar_forces
.
push_back
(
colvarvalue
());
colvar_forces
.
back
().
type
(
cv
->
value
());
// make sure each force is initialized to zero
colvar_forces
.
back
().
reset
();
cv
->
biases
.
push_back
(
this
);
// add back-reference to this bias to colvar
// Add dependency link.
// All biases need at least the value of each colvar
// although possibly not at all timesteps
add_child
(
cv
);
}
else
{
cvm
::
error
(
"Error: cannot find a colvar named
\"
"
+
cv_name
+
"
\"
.
\n
"
,
INPUT_ERROR
);
return
INPUT_ERROR
;
}
return
COLVARS_OK
;
}
int
colvarbias
::
update
()
{
// Note: if anything is added here, it should be added also in the SMP block of calc_biases()
// TODO move here debug msg of bias update
has_data
=
true
;
return
COLVARS_OK
;
}
void
colvarbias
::
communicate_forces
()
{
for
(
size_t
i
=
0
;
i
<
colvars
.
size
();
i
++
)
{
if
(
cvm
::
debug
())
{
cvm
::
log
(
"Communicating a force to colvar
\"
"
+
colvars
[
i
]
->
name
+
"
\"
.
\n
"
);
}
colvars
[
i
]
->
add_bias_force
(
colvar_forces
[
i
]);
}
}
void
colvarbias
::
change_configuration
(
std
::
string
const
&
conf
)
{
cvm
::
error
(
"Error: change_configuration() not implemented.
\n
"
);
}
cvm
::
real
colvarbias
::
energy_difference
(
std
::
string
const
&
conf
)
{
cvm
::
error
(
"Error: energy_difference() not implemented.
\n
"
);
return
0.
;
}
// So far, these are only implemented in colvarbias_abf
int
colvarbias
::
bin_num
()
{
cvm
::
error
(
"Error: bin_num() not implemented.
\n
"
);
return
COLVARS_NOT_IMPLEMENTED
;
}
int
colvarbias
::
current_bin
()
{
cvm
::
error
(
"Error: current_bin() not implemented.
\n
"
);
return
COLVARS_NOT_IMPLEMENTED
;
}
int
colvarbias
::
bin_count
(
int
bin_index
)
{
cvm
::
error
(
"Error: bin_count() not implemented.
\n
"
);
return
COLVARS_NOT_IMPLEMENTED
;
}
int
colvarbias
::
replica_share
()
{
cvm
::
error
(
"Error: replica_share() not implemented.
\n
"
);
return
COLVARS_NOT_IMPLEMENTED
;
}
std
::
ostream
&
colvarbias
::
write_traj_label
(
std
::
ostream
&
os
)
{
os
<<
" "
;
if
(
b_output_energy
)
os
<<
" E_"
<<
cvm
::
wrap_string
(
this
->
name
,
cvm
::
en_width
-
2
);
return
os
;
}
std
::
ostream
&
colvarbias
::
write_traj
(
std
::
ostream
&
os
)
{
os
<<
" "
;
if
(
b_output_energy
)
os
<<
" "
<<
bias_energy
;
return
os
;
}
// Static members
std
::
vector
<
colvardeps
::
feature
*>
colvarbias
::
cvb_features
;
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