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Created
Wed, Aug 28, 01:06
Size
10 KB
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text/x-c
Expires
Fri, Aug 30, 01:06 (2 d)
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blob
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20174267
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rLAMMPS lammps
colvarscript.cpp
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// -*- c++ -*-
#include <cstdlib>
#include <stdlib.h>
#include <string.h>
#include "colvarscript.h"
colvarscript
::
colvarscript
(
colvarproxy
*
p
)
:
proxy
(
p
),
colvars
(
p
->
colvars
),
proxy_error
(
0
)
{
}
/// Run method based on given arguments
int
colvarscript
::
run
(
int
argc
,
char
const
*
argv
[])
{
result
=
""
;
if
(
cvm
::
debug
())
{
cvm
::
log
(
"Called script run with "
+
cvm
::
to_str
(
argc
)
+
" args"
);
for
(
int
i
=
0
;
i
<
argc
;
i
++
)
{
cvm
::
log
(
argv
[
i
]);
}
}
if
(
argc
<
2
)
{
result
=
help_string
();
return
COLVARSCRIPT_OK
;
}
std
::
string
cmd
=
argv
[
1
];
if
(
cmd
==
"colvar"
)
{
return
proc_colvar
(
argc
-
1
,
&
(
argv
[
1
]));
}
if
(
cmd
==
"bias"
)
{
return
proc_bias
(
argc
-
1
,
&
(
argv
[
1
]));
}
if
(
cmd
==
"version"
)
{
result
=
COLVARS_VERSION
;
return
COLVARSCRIPT_OK
;
}
if
(
cmd
==
"reset"
)
{
/// Delete every child object
colvars
->
reset
();
return
COLVARSCRIPT_OK
;
}
if
(
cmd
==
"delete"
)
{
colvars
->
reset
();
// Note: the delete bit may be ignored by some backends
// it is mostly useful in VMD
colvars
->
set_error_bits
(
DELETE_COLVARS
);
return
COLVARSCRIPT_OK
;
}
if
(
cmd
==
"update"
)
{
colvars
->
calc
();
return
COLVARSCRIPT_OK
;
}
if
(
cmd
==
"list"
)
{
if
(
argc
==
2
)
{
for
(
std
::
vector
<
colvar
*>::
iterator
cvi
=
colvars
->
colvars
.
begin
();
cvi
!=
colvars
->
colvars
.
end
();
++
cvi
)
{
result
+=
(
cvi
==
colvars
->
colvars
.
begin
()
?
""
:
" "
)
+
(
*
cvi
)
->
name
;
}
return
COLVARSCRIPT_OK
;
}
else
if
(
argc
==
3
&&
!
strcmp
(
argv
[
2
],
"biases"
))
{
for
(
std
::
vector
<
colvarbias
*>::
iterator
bi
=
colvars
->
biases
.
begin
();
bi
!=
colvars
->
biases
.
end
();
++
bi
)
{
result
+=
(
bi
==
colvars
->
biases
.
begin
()
?
""
:
" "
)
+
(
*
bi
)
->
name
;
}
return
COLVARSCRIPT_OK
;
}
else
{
result
=
"Wrong arguments to command
\"
list
\"\n
"
+
help_string
();
return
COLVARSCRIPT_ERROR
;
}
}
/// Parse config from file
if
(
cmd
==
"configfile"
)
{
if
(
argc
<
3
)
{
result
=
"Missing arguments
\n
"
+
help_string
();
return
COLVARSCRIPT_ERROR
;
}
if
(
colvars
->
read_config_file
(
argv
[
2
])
==
COLVARS_OK
)
{
return
COLVARSCRIPT_OK
;
}
else
{
result
=
"Error parsing configuration file"
;
return
COLVARSCRIPT_ERROR
;
}
}
/// Parse config from string
if
(
cmd
==
"config"
)
{
if
(
argc
<
3
)
{
result
=
"Missing arguments
\n
"
+
help_string
();
return
COLVARSCRIPT_ERROR
;
}
std
::
string
conf
=
argv
[
2
];
if
(
colvars
->
read_config_string
(
conf
)
==
COLVARS_OK
)
{
return
COLVARSCRIPT_OK
;
}
else
{
result
=
"Error parsing configuration string"
;
return
COLVARSCRIPT_ERROR
;
}
}
/// Load an input state file
if
(
cmd
==
"load"
)
{
if
(
argc
<
3
)
{
result
=
"Missing arguments
\n
"
+
help_string
();
return
COLVARSCRIPT_ERROR
;
}
proxy
->
input_prefix_str
=
argv
[
2
];
if
(
colvars
->
setup_input
()
==
COLVARS_OK
)
{
return
COLVARSCRIPT_OK
;
}
else
{
result
=
"Error loading state file"
;
return
COLVARSCRIPT_ERROR
;
}
}
/// Save to an output state file
if
(
cmd
==
"save"
)
{
if
(
argc
<
3
)
{
result
=
"Missing arguments"
;
return
COLVARSCRIPT_ERROR
;
}
proxy
->
output_prefix_str
=
argv
[
2
];
int
error
=
0
;
error
|=
colvars
->
setup_output
();
error
|=
colvars
->
write_output_files
();
return
error
?
COLVARSCRIPT_ERROR
:
COLVARSCRIPT_OK
;
}
/// Print the values that would go on colvars.traj
if
(
cmd
==
"printframelabels"
)
{
std
::
ostringstream
os
;
colvars
->
write_traj_label
(
os
);
result
=
os
.
str
();
return
COLVARSCRIPT_OK
;
}
if
(
cmd
==
"printframe"
)
{
std
::
ostringstream
os
;
colvars
->
write_traj
(
os
);
result
=
os
.
str
();
return
COLVARSCRIPT_OK
;
}
if
(
cmd
==
"frame"
)
{
if
(
argc
==
2
)
{
int
f
=
proxy
->
frame
();
if
(
f
>=
0
)
{
result
=
cvm
::
to_str
(
f
);
return
COLVARSCRIPT_OK
;
}
else
{
result
=
"Frame number is not available"
;
return
COLVARSCRIPT_ERROR
;
}
}
else
if
(
argc
==
3
)
{
// Failure of this function does not trigger an error, but
// returns the plain result to let scripts detect available frames
long
int
f
=
proxy
->
frame
(
strtol
(
argv
[
2
],
NULL
,
10
));
colvars
->
it
=
proxy
->
frame
();
result
=
cvm
::
to_str
(
f
);
return
COLVARSCRIPT_OK
;
}
else
{
result
=
"Wrong arguments to command
\"
frame
\"\n
"
+
help_string
();
return
COLVARSCRIPT_ERROR
;
}
}
result
=
"Syntax error
\n
"
+
help_string
();
return
COLVARSCRIPT_ERROR
;
}
int
colvarscript
::
proc_colvar
(
int
argc
,
char
const
*
argv
[])
{
if
(
argc
<
3
)
{
result
=
"Missing parameters
\n
"
+
help_string
();
return
COLVARSCRIPT_ERROR
;
}
std
::
string
name
=
argv
[
1
];
colvar
*
cv
=
cvm
::
colvar_by_name
(
name
);
if
(
cv
==
NULL
)
{
result
=
"Colvar not found: "
+
name
;
return
COLVARSCRIPT_ERROR
;
}
std
::
string
subcmd
=
argv
[
2
];
if
(
subcmd
==
"value"
)
{
result
=
(
cv
->
value
()).
to_simple_string
();
return
COLVARSCRIPT_OK
;
}
if
(
subcmd
==
"width"
)
{
result
=
cvm
::
to_str
(
cv
->
width
,
0
,
cvm
::
cv_prec
);
return
COLVARSCRIPT_OK
;
}
if
(
subcmd
==
"type"
)
{
result
=
cv
->
value
().
type_desc
(
cv
->
value
().
value_type
);
return
COLVARSCRIPT_OK
;
}
if
(
subcmd
==
"update"
)
{
cv
->
calc
();
cv
->
update
();
result
=
(
cv
->
value
()).
to_simple_string
();
return
COLVARSCRIPT_OK
;
}
if
(
subcmd
==
"delete"
)
{
if
(
cv
->
biases
.
size
()
>
0
)
{
result
=
"Cannot delete a colvar currently used by biases, delete those biases first"
;
return
COLVARSCRIPT_ERROR
;
}
// colvar destructor is tasked with the cleanup
delete
cv
;
// TODO this could be done by the destructors
colvars
->
write_traj_label
(
colvars
->
cv_traj_os
);
return
COLVARSCRIPT_OK
;
}
if
(
subcmd
==
"getconfig"
)
{
result
=
cv
->
get_config
();
return
COLVARSCRIPT_OK
;
}
if
(
subcmd
==
"addforce"
)
{
if
(
argc
<
4
)
{
result
=
"addforce: missing parameter: force value
\n
"
+
help_string
();
return
COLVARSCRIPT_ERROR
;
}
std
::
string
f_str
=
argv
[
3
];
std
::
istringstream
is
(
f_str
);
is
.
width
(
cvm
::
cv_width
);
is
.
precision
(
cvm
::
cv_prec
);
colvarvalue
force
(
cv
->
value
());
force
.
is_derivative
();
if
(
force
.
from_simple_string
(
is
.
str
())
!=
COLVARS_OK
)
{
result
=
"addforce : error parsing force value"
;
return
COLVARSCRIPT_ERROR
;
}
cv
->
add_bias_force
(
force
);
result
=
force
.
to_simple_string
();
return
COLVARSCRIPT_OK
;
}
if
(
subcmd
==
"cvcflags"
)
{
if
(
argc
<
4
)
{
result
=
"cvcflags: missing parameter: vector of flags"
;
return
COLVARSCRIPT_ERROR
;
}
std
::
string
flags_str
=
argv
[
3
];
std
::
istringstream
is
(
flags_str
);
std
::
vector
<
bool
>
flags
;
int
flag
;
while
(
is
>>
flag
)
{
flags
.
push_back
(
flag
!=
0
);
}
int
res
=
cv
->
set_cvc_flags
(
flags
);
if
(
res
!=
COLVARS_OK
)
{
result
=
"Error setting CVC flags"
;
return
COLVARSCRIPT_ERROR
;
}
result
=
"0"
;
return
COLVARSCRIPT_OK
;
}
result
=
"Syntax error
\n
"
+
help_string
();
return
COLVARSCRIPT_ERROR
;
}
int
colvarscript
::
proc_bias
(
int
argc
,
char
const
*
argv
[])
{
if
(
argc
<
3
)
{
result
=
"Missing parameters
\n
"
+
help_string
();
return
COLVARSCRIPT_ERROR
;
}
std
::
string
name
=
argv
[
1
];
colvarbias
*
b
=
cvm
::
bias_by_name
(
name
);
if
(
b
==
NULL
)
{
result
=
"Bias not found: "
+
name
;
return
COLVARSCRIPT_ERROR
;
}
std
::
string
subcmd
=
argv
[
2
];
if
(
subcmd
==
"energy"
)
{
result
=
cvm
::
to_str
(
b
->
get_energy
());
return
COLVARSCRIPT_OK
;
}
if
(
subcmd
==
"update"
)
{
b
->
update
();
result
=
cvm
::
to_str
(
b
->
get_energy
());
return
COLVARSCRIPT_OK
;
}
if
(
subcmd
==
"getconfig"
)
{
result
=
b
->
get_config
();
return
COLVARSCRIPT_OK
;
}
// Subcommands for MW ABF
if
(
subcmd
==
"bin"
)
{
int
r
=
b
->
current_bin
();
result
=
cvm
::
to_str
(
r
);
return
COLVARSCRIPT_OK
;
}
if
(
subcmd
==
"binnum"
)
{
int
r
=
b
->
bin_num
();
if
(
r
<
0
)
{
result
=
"Error: calling bin_num() for bias "
+
b
->
name
;
return
COLVARSCRIPT_ERROR
;
}
result
=
cvm
::
to_str
(
r
);
return
COLVARSCRIPT_OK
;
}
if
(
subcmd
==
"share"
)
{
int
r
=
b
->
replica_share
();
if
(
r
<
0
)
{
result
=
"Error: calling replica_share() for bias "
+
b
->
name
;
return
COLVARSCRIPT_ERROR
;
}
result
=
cvm
::
to_str
(
r
);
return
COLVARSCRIPT_OK
;
}
// End commands for MW ABF
if
(
subcmd
==
"delete"
)
{
// the bias destructor takes care of the cleanup at cvm level
delete
b
;
// TODO this could be done by the destructors
colvars
->
write_traj_label
(
colvars
->
cv_traj_os
);
return
COLVARSCRIPT_OK
;
}
if
(
argc
>=
4
)
{
std
::
string
param
=
argv
[
3
];
if
(
subcmd
==
"count"
)
{
int
index
;
if
(
!
(
std
::
istringstream
(
param
)
>>
index
))
{
result
=
"bin_count: error parsing bin index"
;
return
COLVARSCRIPT_ERROR
;
}
result
=
cvm
::
to_str
(
b
->
bin_count
(
index
));
return
COLVARSCRIPT_OK
;
}
result
=
"Syntax error
\n
"
+
help_string
();
return
COLVARSCRIPT_ERROR
;
}
result
=
"Syntax error
\n
"
+
help_string
();
return
COLVARSCRIPT_ERROR
;
}
std
::
string
colvarscript
::
help_string
()
{
std
::
string
buf
;
buf
=
"Usage: cv <subcommand> [args...]
\n
\
\n
\
Managing the colvars module:
\n
\
configfile <file name> -- read configuration from a file
\n
\
config <string> -- read configuration from the given string
\n
\
reset -- delete all internal configuration
\n
\
delete -- delete this colvars module instance
\n
\
version -- return version of colvars code
\n
\
\n
\
Input and output:
\n
\
list -- return a list of all variables
\n
\
list biases -- return a list of all biases
\n
\
load <file name> -- load a state file (requires configuration)
\n
\
update -- recalculate colvars and biases based
\n
\
printframe -- return a summary of the current frame
\n
\
printframelabels -- return labels to annotate printframe's output
\n
"
;
if
(
proxy
->
frame
()
!=
COLVARS_NOT_IMPLEMENTED
)
{
buf
+=
"\
frame -- return current frame number
\n
\
frame <new_frame> -- set frame number
\n
"
;
}
buf
+=
"
\n
\
Accessing collective variables:
\n
\
colvar <name> value -- return the current value of colvar <name>
\n
\
colvar <name> update -- recalculate colvar <name>
\n
\
colvar <name> type -- return the type of colvar <name>
\n
\
colvar <name> delete -- delete colvar <name>
\n
\
colvar <name> addforce <F> -- apply given force on colvar <name>
\n
\
colvar <name> getconfig -- return config string of colvar <name>
\n
\
\n
\
Accessing biases:
\n
\
bias <name> energy -- return the current energy of bias <name>
\n
\
bias <name> update -- recalculate bias <name>
\n
\
bias <name> delete -- delete bias <name>
\n
\
bias <name> getconfig -- return config string of bias <name>
\n
"
;
return
buf
;
}
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