Skip to content
GitLab
Explore
Sign in
Primary navigation
Search or go to…
Project
S
soap-plus-plus
Manage
Activity
Members
Labels
Plan
Issues
Issue boards
Milestones
Wiki
Code
Merge requests
Repository
Branches
Commits
Tags
Repository graph
Compare revisions
Build
Pipelines
Jobs
Pipeline schedules
Artifacts
Deploy
Releases
Container registry
Model registry
Operate
Environments
Monitor
Incidents
Service Desk
Analyze
Value stream analytics
Contributor analytics
CI/CD analytics
Repository analytics
Model experiments
Help
Help
Support
GitLab documentation
Compare GitLab plans
Community forum
Contribute to GitLab
Provide feedback
Keyboard shortcuts
?
Snippets
Groups
Projects
Show more breadcrumbs
nomad-lab
soap-plus-plus
Commits
c1a1e4cd
Commit
c1a1e4cd
authored
8 years ago
by
Carl Poelking
Browse files
Options
Downloads
Patches
Plain Diff
Valence charge density added.
parent
ad9f37a5
Branches
Branches containing commit
Tags
0.1.0
Tags containing commit
No related merge requests found
Changes
3
Hide whitespace changes
Inline
Side-by-side
Showing
3 changed files
src/soap/boundary.hpp
+0
-1
0 additions, 1 deletion
src/soap/boundary.hpp
src/soap/soapy/elements.py
+19
-7
19 additions, 7 deletions
src/soap/soapy/elements.py
src/soap/soapy/lagraph.py
+6
-0
6 additions, 0 deletions
src/soap/soapy/lagraph.py
with
25 additions
and
8 deletions
src/soap/boundary.hpp
+
0
−
1
View file @
c1a1e4cd
...
@@ -76,7 +76,6 @@ public:
...
@@ -76,7 +76,6 @@ public:
_box
.
ZeroMatrix
();
_box
.
ZeroMatrix
();
}
}
vec
connect
(
const
vec
&
r_i
,
const
vec
&
r_j
)
const
{
vec
connect
(
const
vec
&
r_i
,
const
vec
&
r_j
)
const
{
std
::
cout
<<
"connect open"
<<
std
::
endl
;
return
r_j
-
r_i
;
return
r_j
-
r_i
;
}
}
template
<
class
Archive
>
template
<
class
Archive
>
...
...
This diff is collapsed.
Click to expand it.
src/soap/soapy/elements.py
+
19
−
7
View file @
c1a1e4cd
...
@@ -48,6 +48,17 @@ class PeriodicTable(object):
...
@@ -48,6 +48,17 @@ class PeriodicTable(object):
1.570
,
1.560
,
2.000
,
1.560
,
1.440
,
1.340
,
1.300
,
1.280
,
1.260
,
1.270
,
1.300
,
1.340
,
1.490
,
1.480
,
1.470
,
1.460
,
1.460
,
1.570
,
1.560
,
2.000
,
1.560
,
1.440
,
1.340
,
1.300
,
1.280
,
1.260
,
1.270
,
1.300
,
1.340
,
1.490
,
1.480
,
1.470
,
1.460
,
1.460
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
1.650
,
2.000
,
1.420
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
1.650
,
2.000
,
1.420
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
]
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
,
2.000
]
element_valence
=
[
-
1.
,
1
,
-
1
,
1
,
2
,
3
,
4
,
3
,
2
,
1
,
-
1
,
1
,
2
,
3
,
4
,
3
,
2
,
1
,
-
1
,
1
,
2
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
,
-
1
]
def
__init__
(
self
):
def
__init__
(
self
):
self
.
elements_by_z
=
{}
self
.
elements_by_z
=
{}
self
.
elements_by_name
=
{}
self
.
elements_by_name
=
{}
...
@@ -60,13 +71,13 @@ class PeriodicTable(object):
...
@@ -60,13 +71,13 @@ class PeriodicTable(object):
raise
RuntimeError
(
"
Invalid element identifier
'
%s
'"
%
key
)
raise
RuntimeError
(
"
Invalid element identifier
'
%s
'"
%
key
)
def
setup
(
self
):
def
setup
(
self
):
element_z
=
[
i
for
i
in
range
(
len
(
self
.
element_names
))
]
element_z
=
[
i
for
i
in
range
(
len
(
self
.
element_names
))
]
assert
len
(
self
.
element_names
)
==
len
(
self
.
element_mass
)
==
len
(
self
.
element_covrad
)
assert
len
(
self
.
element_names
)
==
len
(
self
.
element_mass
)
==
len
(
self
.
element_covrad
)
==
len
(
self
.
element_valence
)
for
z
,
name
,
mass
,
covrad
,
elneg
in
zip
(
element_z
,
self
.
element_names
,
self
.
element_mass
,
self
.
element_covrad
,
self
.
element_elneg
):
for
z
,
name
,
mass
,
covrad
,
elneg
,
valence
in
zip
(
element_z
,
self
.
element_names
,
self
.
element_mass
,
self
.
element_covrad
,
self
.
element_elneg
,
self
.
element_valence
):
name
=
name
.
strip
()
name
=
name
.
strip
()
self
.
addElement
(
z
,
name
,
mass
,
covrad
,
elneg
)
self
.
addElement
(
z
,
name
,
mass
,
covrad
,
elneg
,
valence
)
return
self
return
self
def
addElement
(
self
,
z
,
name
,
mass
,
covrad
,
elneg
):
def
addElement
(
self
,
z
,
name
,
mass
,
covrad
,
elneg
,
valence
):
elem
=
AtomicElement
(
z
,
name
,
mass
,
covrad
,
elneg
)
elem
=
AtomicElement
(
z
,
name
,
mass
,
covrad
,
elneg
,
valence
)
self
.
elements_by_z
[
z
]
=
elem
self
.
elements_by_z
[
z
]
=
elem
self
.
elements_by_name
[
name
]
=
elem
self
.
elements_by_name
[
name
]
=
elem
return
return
...
@@ -77,13 +88,14 @@ class PeriodicTable(object):
...
@@ -77,13 +88,14 @@ class PeriodicTable(object):
return
props
return
props
class
AtomicElement
(
object
):
class
AtomicElement
(
object
):
def
__init__
(
self
,
z
,
name
,
mass
,
covrad
,
elneg
):
def
__init__
(
self
,
z
,
name
,
mass
,
covrad
,
elneg
,
valence
):
self
.
z
=
z
self
.
z
=
z
self
.
name
=
name
self
.
name
=
name
self
.
mass
=
mass
self
.
mass
=
mass
self
.
covrad
=
covrad
self
.
covrad
=
covrad
self
.
elneg
=
elneg
self
.
elneg
=
elneg
self
.
property_dict
=
{
'
z
'
:
z
,
'
covrad
'
:
covrad
,
'
name
'
:
name
,
'
mass
'
:
mass
,
'
elneg
'
:
elneg
}
self
.
valence
=
valence
self
.
property_dict
=
{
'
z
'
:
z
,
'
covrad
'
:
covrad
,
'
name
'
:
name
,
'
mass
'
:
mass
,
'
elneg
'
:
elneg
,
'
valence
'
:
valence
}
def
__getitem__
(
self
,
key
):
def
__getitem__
(
self
,
key
):
return
self
.
property_dict
[
key
]
return
self
.
property_dict
[
key
]
...
...
This diff is collapsed.
Click to expand it.
src/soap/soapy/lagraph.py
+
6
−
0
View file @
c1a1e4cd
...
@@ -601,6 +601,12 @@ class ParticleGraph(object):
...
@@ -601,6 +601,12 @@ class ParticleGraph(object):
charge_map
=
{}
charge_map
=
{}
for
elem
in
soap
.
soapy
.
elements
.
PeriodicTable
.
element_names
:
for
elem
in
soap
.
soapy
.
elements
.
PeriodicTable
.
element_names
:
charge_map
[
elem
]
=
1.
charge_map
[
elem
]
=
1.
elif
density_type
==
"
number_density_generic
"
:
charge_map
=
{}
for
elem
in
soap
.
soapy
.
elements
.
PeriodicTable
.
element_names
:
charge_map
[
elem
]
=
1.
elif
density_type
==
"
valence_charge_density
"
:
charge_map
=
soap
.
soapy
.
elements
.
periodic_table
.
getPropertyDict
(
"
valence
"
)
else
:
else
:
raise
NotImplementedError
(
"
Density type
'
%s
'"
%
density_type
)
raise
NotImplementedError
(
"
Density type
'
%s
'"
%
density_type
)
# ... Apply
# ... Apply
...
...
This diff is collapsed.
Click to expand it.
Preview
0%
Loading
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Save comment
Cancel
Please
register
or
sign in
to comment