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Martin Kurečka
Plumed AlphaFold
Commits
13a16bea
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Commit
13a16bea
authored
8 years ago
by
Giovanni Bussi
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Replaces @multi with @replicas
As requested by @gtribello (see #221)
parent
855a6f3f
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Changes
3
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3 changed files
regtest/basic/rt-multi-1/plumed.dat
+5
-5
5 additions, 5 deletions
regtest/basic/rt-multi-1/plumed.dat
src/tools/Tools.cpp
+1
-1
1 addition, 1 deletion
src/tools/Tools.cpp
src/tools/Tools.h
+1
-1
1 addition, 1 deletion
src/tools/Tools.h
with
7 additions
and
7 deletions
regtest/basic/rt-multi-1/plumed.dat
+
5
−
5
View file @
13a16bea
...
@@ -3,18 +3,18 @@ p1: POSITION ATOM=1
...
@@ -3,18 +3,18 @@ p1: POSITION ATOM=1
p2: POSITION ATOM=2
p2: POSITION ATOM=2
# different coefficients in different replicas
# different coefficients in different replicas
f: COMBINE ARG=d,p1.x,p2.y COEFFICIENTS=@
multi
:{{1,2,3} {0,0,0} {2,4,6}} PERIODIC=NO
f: COMBINE ARG=d,p1.x,p2.y COEFFICIENTS=@
replicas
:{{1,2,3} {0,0,0} {2,4,6}} PERIODIC=NO
PRINT ARG=f FILE=colvar
PRINT ARG=f FILE=colvar
# equivalent syntax:
# equivalent syntax:
#g: COMBINE ARG=d,p1.x,p2.y COEFFICIENTS=@
multi
:{{1,2,3} {1,0,3} {1,4,3}} PERIODIC=NO
#g: COMBINE ARG=d,p1.x,p2.y COEFFICIENTS=@
replicas
:{{1,2,3} {1,0,3} {1,4,3}} PERIODIC=NO
g: COMBINE ARG=d,p1.x,p2.y COEFFICIENTS={1 @
multi
:{2 0 4} 3} PERIODIC=NO
g: COMBINE ARG=d,p1.x,p2.y COEFFICIENTS={1 @
replicas
:{2 0 4} 3} PERIODIC=NO
PRINT ARG=g FILE=colvarg
PRINT ARG=g FILE=colvarg
# different arguments in different replicas
# different arguments in different replicas
PRINT ARG=@
multi
:{d,p1.x,p2.x} FILE=multi
PRINT ARG=@
replicas
:{d,p1.x,p2.x} FILE=multi
# typical umbrella sampling stuff
# typical umbrella sampling stuff
RESTRAINT ARG=d AT=@
multi
:{1,2,3} KAPPA=100
RESTRAINT ARG=d AT=@
replicas
:{1,2,3} KAPPA=100
This diff is collapsed.
Click to expand it.
src/tools/Tools.cpp
+
1
−
1
View file @
13a16bea
...
@@ -220,7 +220,7 @@ bool Tools::getKey(vector<string>& line,const string & key,string & s,int rep){
...
@@ -220,7 +220,7 @@ bool Tools::getKey(vector<string>& line,const string & key,string & s,int rep){
string
tmp
=
(
*
p
).
substr
(
key
.
length
(),(
*
p
).
length
());
string
tmp
=
(
*
p
).
substr
(
key
.
length
(),(
*
p
).
length
());
line
.
erase
(
p
);
line
.
erase
(
p
);
s
=
tmp
;
s
=
tmp
;
const
std
::
string
multi
(
"@
multi
:"
);
const
std
::
string
multi
(
"@
replicas
:"
);
if
(
rep
>=
0
&&
startWith
(
s
,
multi
)){
if
(
rep
>=
0
&&
startWith
(
s
,
multi
)){
s
=
s
.
substr
(
multi
.
length
(),
s
.
length
());
s
=
s
.
substr
(
multi
.
length
(),
s
.
length
());
std
::
vector
<
std
::
string
>
words
=
getWords
(
s
,
"
\t\n
,"
);
std
::
vector
<
std
::
string
>
words
=
getWords
(
s
,
"
\t\n
,"
);
...
...
This diff is collapsed.
Click to expand it.
src/tools/Tools.h
+
1
−
1
View file @
13a16bea
...
@@ -155,7 +155,7 @@ bool Tools::parseVector(std::vector<std::string>&line,const std::string&key,std:
...
@@ -155,7 +155,7 @@ bool Tools::parseVector(std::vector<std::string>&line,const std::string&key,std:
for
(
unsigned
i
=
0
;
i
<
words
.
size
();
++
i
){
for
(
unsigned
i
=
0
;
i
<
words
.
size
();
++
i
){
T
v
;
T
v
;
std
::
string
s
=
words
[
i
];
std
::
string
s
=
words
[
i
];
const
std
::
string
multi
(
"@
multi
:"
);
const
std
::
string
multi
(
"@
replicas
:"
);
if
(
rep
>=
0
&&
startWith
(
s
,
multi
)){
if
(
rep
>=
0
&&
startWith
(
s
,
multi
)){
s
=
s
.
substr
(
multi
.
length
(),
s
.
length
());
s
=
s
.
substr
(
multi
.
length
(),
s
.
length
());
std
::
vector
<
std
::
string
>
words
=
getWords
(
s
,
"
\t\n
,"
);
std
::
vector
<
std
::
string
>
words
=
getWords
(
s
,
"
\t\n
,"
);
...
...
This diff is collapsed.
Click to expand it.
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