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James Graham
pycgtool
Commits
ab22ad42
Commit
ab22ad42
authored
8 years ago
by
James Graham
Browse files
Options
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Patches
Plain Diff
Remove empirical_scale and factor_2 from options
They were useful during testing, but are now unnecessary
parent
fad8ceb0
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Changes
4
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4 changed files
doc/tutorial_files/md.mdp
+0
-1
0 additions, 1 deletion
doc/tutorial_files/md.mdp
pycgtool.py
+0
-2
0 additions, 2 deletions
pycgtool.py
pycgtool/bondset.py
+2
-17
2 additions, 17 deletions
pycgtool/bondset.py
test/test_pycgtool.py
+1
-1
1 addition, 1 deletion
test/test_pycgtool.py
with
3 additions
and
21 deletions
doc/tutorial_files/md.mdp
+
0
−
1
View file @
ab22ad42
...
@@ -29,7 +29,6 @@ nstxout-compressed = 1000
...
@@ -29,7 +29,6 @@ nstxout-compressed = 1000
compressed-x-precision = 100
compressed-x-precision = 100
compressed-x-grps = System
compressed-x-grps = System
energygrps = System
energygrps = System
imd-group = Other
; NEIGHBOURLIST and MARTINI
; NEIGHBOURLIST and MARTINI
; To achieve faster simulations in combination with the Verlet-neighborlist
; To achieve faster simulations in combination with the Verlet-neighborlist
...
...
This diff is collapsed.
Click to expand it.
pycgtool.py
+
0
−
2
View file @
ab22ad42
...
@@ -39,8 +39,6 @@ if __name__ == "__main__":
...
@@ -39,8 +39,6 @@ if __name__ == "__main__":
(
"
default_fc
"
,
False
),
(
"
default_fc
"
,
False
),
(
"
generate_angles
"
,
True
),
(
"
generate_angles
"
,
True
),
(
"
generate_dihedrals
"
,
False
),
(
"
generate_dihedrals
"
,
False
),
(
"
empirical_corr
"
,
False
),
(
"
factor_two
"
,
1
),
(
"
length_form
"
,
"
harmonic
"
),
(
"
length_form
"
,
"
harmonic
"
),
(
"
angle_form
"
,
"
cosharmonic
"
),
(
"
angle_form
"
,
"
cosharmonic
"
),
(
"
dihedral_form
"
,
"
harmonic
"
)
(
"
dihedral_form
"
,
"
harmonic
"
)
...
...
This diff is collapsed.
Click to expand it.
pycgtool/bondset.py
+
2
−
17
View file @
ab22ad42
...
@@ -105,14 +105,6 @@ class BondSet:
...
@@ -105,14 +105,6 @@ class BondSet:
self
.
_fconst_constr_threshold
=
options
.
constr_threshold
self
.
_fconst_constr_threshold
=
options
.
constr_threshold
self
.
_empirical_correction_factor
=
1.
try
:
self
.
_empirical_correction
=
options
.
empirical_corr
if
self
.
_empirical_correction
:
self
.
_empirical_correction_factor
=
1.05
except
AttributeError
:
self
.
_empirical_correction
=
False
try
:
try
:
self
.
_temperature
=
options
.
temperature
self
.
_temperature
=
options
.
temperature
except
AttributeError
:
except
AttributeError
:
...
@@ -123,11 +115,6 @@ class BondSet:
...
@@ -123,11 +115,6 @@ class BondSet:
except
AttributeError
:
except
AttributeError
:
self
.
_default_fc
=
False
self
.
_default_fc
=
False
try
:
self
.
_factor_two
=
options
.
factor_two
except
AttributeError
:
self
.
_factor_two
=
1
functional_forms
=
FunctionalForms
()
functional_forms
=
FunctionalForms
()
self
.
_functional_forms
=
{}
self
.
_functional_forms
=
{}
try
:
try
:
...
@@ -290,12 +277,10 @@ class BondSet:
...
@@ -290,12 +277,10 @@ class BondSet:
print
(
"
\n
[ {0:s} ]
"
.
format
(
section_header
),
file
=
itp
)
print
(
"
\n
[ {0:s} ]
"
.
format
(
section_header
),
file
=
itp
)
for
bond
in
bonds
:
for
bond
in
bonds
:
# Factor is usually 1, unless doing correction
# Factor is usually 1, unless doing correction
eqm
=
bond
.
eqm
*
self
.
_empirical_correction_factor
fconst
=
bond
.
fconst
*
self
.
_empirical_correction_factor
line
=
"
"
.
join
([
"
{0:4d}
"
.
format
(
atnum
+
1
)
for
atnum
in
bond
.
atom_numbers
])
line
=
"
"
.
join
([
"
{0:4d}
"
.
format
(
atnum
+
1
)
for
atnum
in
bond
.
atom_numbers
])
line
+=
"
{0:4d} {1:12.5f}
"
.
format
(
1
,
eqm
)
line
+=
"
{0:4d} {1:12.5f}
"
.
format
(
1
,
bond
.
eqm
)
if
print_fconst
:
if
print_fconst
:
line
+=
"
{0:12.5f}
"
.
format
(
fconst
)
line
+=
"
{0:12.5f}
"
.
format
(
bond
.
fconst
)
if
multiplicity
is
not
None
:
if
multiplicity
is
not
None
:
line
+=
"
{0:4d}
"
.
format
(
multiplicity
)
line
+=
"
{0:4d}
"
.
format
(
multiplicity
)
print
(
line
,
file
=
itp
)
print
(
line
,
file
=
itp
)
...
...
This diff is collapsed.
Click to expand it.
test/test_pycgtool.py
+
1
−
1
View file @
ab22ad42
...
@@ -37,7 +37,7 @@ class PycgtoolTest(unittest.TestCase):
...
@@ -37,7 +37,7 @@ class PycgtoolTest(unittest.TestCase):
(
"
map_center
"
,
"
geom
"
),
(
"
map_center
"
,
"
geom
"
),
(
"
constr_threshold
"
,
100000
),
(
"
constr_threshold
"
,
100000
),
(
"
dump_measurements
"
,
False
),
(
"
dump_measurements
"
,
False
),
(
"
dump_n_values
"
,
10000
0
),
(
"
dump_n_values
"
,
10000
),
(
"
output_forcefield
"
,
False
),
(
"
output_forcefield
"
,
False
),
(
"
temperature
"
,
310
),
(
"
temperature
"
,
310
),
(
"
default_fc
"
,
False
),
(
"
default_fc
"
,
False
),
...
...
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Click to expand it.
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