Configuration and use of casm view
The casm view command is a shortcut for viewing CASM configurations in visualization software, such as VESTA.
It writes POSCAR files for one or more configurations and runs a subcommand to launch a visualization program that can view those files.
Often it is used with VESTA though it could be configured to work with other software.
Example usage
- Note proper configuration depends on having VESTA installed and accessible as this example configures it. It may need to be customized for your system
This example will:
- Create an example project
- Enumerate configurations in that project
- Configure
casm viewto launch VESTA - View a configuration in VESTA
- View multiple configurations in VESTA at once
import os
import pathlib
import tempfile
tutorials_dir = os.getcwd()
# use a temporary directory for the CASM project
# - change this to where you want to create a project
project_tmpdir = tempfile.TemporaryDirectory()
project_path = pathlib.Path(project_tmpdir.name)
# copy the ZrO prim file to the new project directory
!cp $tutorials_dir/primfiles/ZrO_prim.json $project_path/prim.json
# change the current working directory to the new project directory
%cd $project_path
# initialize the project & set default composition axes
!ccasm init
!ccasm composition --calc && ccasm composition --select 0
# enumerate configurations up to supercell size 4
!ccasm enum -m ConfigEnumAllOccupations --max 4
/private/var/folders/v7/lq3_7hgj7n95d1xrct505ryh0000gp/T/tmpk6cgazo_
***************************
Initializing CASM project 'ZrO'
Creating CASM project directory tree at: "/private/var/folders/v7/lq3_7hgj7n95d1xrct505ryh0000gp/T/tmpk6cgazo_"
Writing prim file: "/private/var/folders/v7/lq3_7hgj7n95d1xrct505ryh0000gp/T/tmpk6cgazo_/.casm/prim.json"
DONE
***************************
Using the PRIM to enumerate standard composition axes for this space.
Possible composition axes:
KEY ORIGIN a GENERAL FORMULA
--- --- --- ---
0 Zr(2)O(2) Zr(2)Va(2) Zr(2)Va(2a)O(2-2a)
1 Zr(2)Va(2) Zr(2)O(2) Zr(2)Va(2-2a)O(2a)
Wrote: "/private/var/folders/v7/lq3_7hgj7n95d1xrct505ryh0000gp/T/tmpk6cgazo_/.casm/composition_axes.json"
Please use 'casm composition --select' to choose your composition axes.
***************************
Possible composition axes:
KEY ORIGIN a GENERAL FORMULA
--- --- --- ---
0 Zr(2)O(2) Zr(2)Va(2) Zr(2)Va(2a)O(2-2a)
1 Zr(2)Va(2) Zr(2)O(2) Zr(2)Va(2-2a)O(2a)
Currently selected composition axes: 0
Parametric composition:
comp(a) = 0.25*comp_n(Va) - 0.25*(comp_n(O) - 2)
Composition:
comp_n(Zr) = 2
comp_n(Va) = 2*comp(a)
comp_n(O) = 2 - 2*comp(a)
Parametric chemical potentials:
param_chem_pot(a) = -2*chem_pot(O)
Wrote: "/private/var/folders/v7/lq3_7hgj7n95d1xrct505ryh0000gp/T/tmpk6cgazo_/.casm/composition_axes.json"
-- Begin: ConfigEnumAllOccupations --
Input from JSON (--input or --setings):
{
}
Input from `casm enum` options:
{
"max" : 4,
"method" : "ConfigEnumAllOccupations"
}
Combined Input:
{
"supercells" : {
"max" : 4
}
}
-- Checking input --
primitive_only: true
filter: false
verbosity: 10
dry_run: false
output_configurations: false
# of initial enumeration states: 20
-- Begin: ConfigEnumAllOccupations enumeration --
# configurations in this project: 0
Begin enumeration
Enumerate configurations for: SCEL1_1_1_1_0_0_0
3 configurations (3 new, 0 excluded by filter).
Enumerate configurations for: SCEL2_1_2_1_0_0_0
4 configurations (4 new, 0 excluded by filter).
Enumerate configurations for: SCEL2_1_2_1_1_0_0
3 configurations (3 new, 0 excluded by filter).
Enumerate configurations for: SCEL2_1_1_2_0_0_0
3 configurations (3 new, 0 excluded by filter).
Enumerate configurations for: SCEL3_3_1_1_0_0_1
10 configurations (10 new, 0 excluded by filter).
Enumerate configurations for: SCEL3_3_1_1_0_0_2
10 configurations (10 new, 0 excluded by filter).
Enumerate configurations for: SCEL3_1_3_1_2_0_0
16 configurations (16 new, 0 excluded by filter).
Enumerate configurations for: SCEL3_3_1_1_0_2_2
10 configurations (10 new, 0 excluded by filter).
Enumerate configurations for: SCEL3_1_1_3_0_0_0
10 configurations (10 new, 0 excluded by filter).
Enumerate configurations for: SCEL4_1_4_1_0_0_0
27 configurations (27 new, 0 excluded by filter).
Enumerate configurations for: SCEL4_2_2_1_0_0_1
27 configurations (27 new, 0 excluded by filter).
Enumerate configurations for: SCEL4_1_4_1_1_0_0
42 configurations (42 new, 0 excluded by filter).
Enumerate configurations for: SCEL4_4_1_1_0_3_2
24 configurations (24 new, 0 excluded by filter).
Enumerate configurations for: SCEL4_1_4_1_2_0_0
24 configurations (24 new, 0 excluded by filter).
Enumerate configurations for: SCEL4_2_2_1_0_1_1
21 configurations (21 new, 0 excluded by filter).
Enumerate configurations for: SCEL4_2_2_1_0_0_0
15 configurations (15 new, 0 excluded by filter).
Enumerate configurations for: SCEL4_2_2_1_0_1_0
18 configurations (18 new, 0 excluded by filter).
Enumerate configurations for: SCEL4_1_2_2_0_0_0
21 configurations (21 new, 0 excluded by filter).
Enumerate configurations for: SCEL4_1_2_2_1_0_0
24 configurations (24 new, 0 excluded by filter).
Enumerate configurations for: SCEL4_1_1_4_0_0_0
24 configurations (24 new, 0 excluded by filter).
Enumeration complete
# new configurations: 336
# configurations in this project: 336
Write supercell database... DONE
Write configuration database... DONE
Create a selection at a particular composition
# view a list of configurations at composition ZrO_{1/6}
atom_frac_O = 1./(6.+1.)
atom_frac_O_plus = atom_frac_O + 0.01
atom_frac_O_minus = atom_frac_O - 0.01
!ccasm select --set 'lt(atom_frac(O),'$atom_frac_O_plus')'
!ccasm select --set-off 'lt(atom_frac(O),'$atom_frac_O_minus')'
!ccasm query -k 'atom_frac(O)' -o STDOUT
-- Input config list: MASTER --
# configs in this project: 336
# configs included in this list: 336
# configs selected in this list: 0
-- set: lt(atom_frac(O),0.15285714285714286) --
selection time: 0.0014823 (s)
-- Write: Selection --
write: "MASTER"
-- Output config list: MASTER --
# configs in this project: 336
# configs included in this list: 336
# configs selected in this list: 19
-- Input config list: MASTER --
# configs in this project: 336
# configs included in this list: 336
# configs selected in this list: 19
-- set-off: lt(atom_frac(O),0.13285714285714284) --
selection time: 0.000152694 (s)
-- Write: Selection --
write: "MASTER"
-- Output config list: MASTER --
# configs in this project: 336
# configs included in this list: 336
# configs selected in this list: 6
Print:
- atom_frac(O)
to "STDOUT"
# name selected atom_frac(O)
SCEL3_1_1_3_0_0_0/0 1 0.14285714
SCEL3_1_3_1_2_0_0/0 1 0.14285714
SCEL3_1_3_1_2_0_0/2 1 0.14285714
SCEL3_3_1_1_0_0_1/0 1 0.14285714
SCEL3_3_1_1_0_0_2/0 1 0.14285714
SCEL3_3_1_1_0_2_2/0 1 0.14285714
-Output printed to terminal, since no output file specified-
DONE.
Reminder:
This is an example configuration of casm view to use VESTA.
- It requires VESTA to be installed
- The correct configuration on your local machine depends on your VESTA installation
- For use on linux, try adjusting the comments to try the linux configuration.
- To check if the configuration is successful, try the following cells
# example osx config:
!ccasm settings --set-view-command \
'casm.view "open -a /Applications/VESTA/VESTA.app"'
# example linux config:
# casm settings --set-view-command ’casm.view VESTA’
Set view command to: 'casm.view "open -a /Applications/VESTA/VESTA.app"'
# This might an interesting configuration to view...
!ccasm view --confignames SCEL3_3_1_1_0_2_2/0
# Note: If the configuration is correct,
# 1 POSCAR will be printed and opened in VESTA
SCEL3_3_1_1_0_2_2/0:
casm.view "open -a /Applications/VESTA/VESTA.app" /private/var/folders/v7/lq3_7hgj7n95d1xrct505ryh0000gp/T/tmpk6cgazo_/.casm/tmp/POSCAR 2>&1
Begin casm.view
Reading POSCAR:
1.00000000
4.85098029 2.80071477 0.00000000
0.00000000 5.60142954 0.00000000
1.61699343 2.80071477 5.16867834
O Zr
1 6
Direct
-0.08333333 0.25000000 0.25000000 O
0.00000000 0.00000000 0.00000000 Zr
0.66666667 0.66666667 0.00000000 Zr
0.33333333 0.33333333 0.00000000 Zr
0.16666667 -0.16666667 0.50000000 Zr
0.83333333 0.50000000 0.50000000 Zr
0.50000000 0.16666667 0.50000000 Zr
# open all selected configurations
!ccasm view --config MASTER
# Note: If the configuration is correct,
# 6 POSCARs will be printed and opened in VESTA
SCEL3_1_1_3_0_0_0/0:
casm.view "open -a /Applications/VESTA/VESTA.app" /private/var/folders/v7/lq3_7hgj7n95d1xrct505ryh0000gp/T/tmpk6cgazo_/.casm/tmp/POSCAR 2>&1
Begin casm.view
Reading POSCAR:
1.00000000
3.23398686 0.00000000 0.00000000
-1.61699343 2.80071477 0.00000000
0.00000000 0.00000000 15.50603502
O Zr
1 6
Direct
0.33333333 0.66666667 0.08333333 O
0.00000000 0.00000000 0.00000000 Zr
0.00000000 0.00000000 0.33333333 Zr
0.00000000 0.00000000 0.66666667 Zr
0.66666667 0.33333333 0.16666667 Zr
0.66666667 0.33333333 0.50000000 Zr
0.66666667 0.33333333 0.83333333 Zr
SCEL3_1_3_1_2_0_0/0:
casm.view "open -a /Applications/VESTA/VESTA.app" /private/var/folders/v7/lq3_7hgj7n95d1xrct505ryh0000gp/T/tmpk6cgazo_/.casm/tmp/POSCAR 2>&1
Begin casm.view
Reading POSCAR:
1.00000000
3.23398686 0.00000000 0.00000000
-1.61699343 2.80071477 -5.16867834
0.00000000 5.60142954 5.16867834
O Zr
1 6
Direct
0.02777778 0.05555556 0.30555556 O
0.00000000 0.00000000 0.00000000 Zr
0.33333333 0.66666667 0.66666667 Zr
0.66666667 0.33333333 0.33333333 Zr
0.38888889 -0.22222222 0.27777778 Zr
0.72222222 0.44444444 0.94444444 Zr
1.05555556 0.11111111 0.61111111 Zr
SCEL3_1_3_1_2_0_0/2:
casm.view "open -a /Applications/VESTA/VESTA.app" /private/var/folders/v7/lq3_7hgj7n95d1xrct505ryh0000gp/T/tmpk6cgazo_/.casm/tmp/POSCAR 2>&1
Begin casm.view
Reading POSCAR:
1.00000000
3.23398686 0.00000000 0.00000000
-1.61699343 2.80071477 -5.16867834
0.00000000 5.60142954 5.16867834
O Zr
1 6
Direct
-0.13888889 -0.27777778 0.47222222 O
0.00000000 0.00000000 0.00000000 Zr
0.33333333 0.66666667 0.66666667 Zr
0.66666667 0.33333333 0.33333333 Zr
0.38888889 -0.22222222 0.27777778 Zr
0.72222222 0.44444444 0.94444444 Zr
1.05555556 0.11111111 0.61111111 Zr
SCEL3_3_1_1_0_0_1/0:
casm.view "open -a /Applications/VESTA/VESTA.app" /private/var/folders/v7/lq3_7hgj7n95d1xrct505ryh0000gp/T/tmpk6cgazo_/.casm/tmp/POSCAR 2>&1
Begin casm.view
Reading POSCAR:
1.00000000
1.61699343 2.80071477 0.00000000
0.00000000 0.00000000 5.16867834
6.46797372 -5.60142954 0.00000000
O Zr
1 6
Direct
0.44444444 0.25000000 -0.11111111 O
0.00000000 0.00000000 0.00000000 Zr
0.33333333 0.00000000 0.66666667 Zr
0.66666667 0.00000000 0.33333333 Zr
0.55555556 0.50000000 0.11111111 Zr
0.88888889 0.50000000 0.77777778 Zr
1.22222222 0.50000000 0.44444444 Zr
SCEL3_3_1_1_0_0_2/0:
casm.view "open -a /Applications/VESTA/VESTA.app" /private/var/folders/v7/lq3_7hgj7n95d1xrct505ryh0000gp/T/tmpk6cgazo_/.casm/tmp/POSCAR 2>&1
Begin casm.view
Reading POSCAR:
1.00000000
0.00000000 0.00000000 5.16867834
4.85098029 2.80071477 0.00000000
-4.85098029 2.80071477 0.00000000
O Zr
1 6
Direct
0.25000000 0.33333333 0.33333333 O
0.00000000 0.00000000 0.00000000 Zr
0.00000000 0.66666667 0.33333333 Zr
0.00000000 0.33333333 0.66666667 Zr
0.50000000 0.33333333 -0.00000000 Zr
0.50000000 1.00000000 0.33333333 Zr
0.50000000 0.66666667 0.66666667 Zr
SCEL3_3_1_1_0_2_2/0:
casm.view "open -a /Applications/VESTA/VESTA.app" /private/var/folders/v7/lq3_7hgj7n95d1xrct505ryh0000gp/T/tmpk6cgazo_/.casm/tmp/POSCAR 2>&1
Begin casm.view
Reading POSCAR:
1.00000000
4.85098029 2.80071477 0.00000000
0.00000000 5.60142954 0.00000000
1.61699343 2.80071477 5.16867834
O Zr
1 6
Direct
-0.08333333 0.25000000 0.25000000 O
0.00000000 0.00000000 0.00000000 Zr
0.66666667 0.66666667 0.00000000 Zr
0.33333333 0.33333333 0.00000000 Zr
0.16666667 -0.16666667 0.50000000 Zr
0.83333333 0.50000000 0.50000000 Zr
0.50000000 0.16666667 0.50000000 Zr