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pyiron
Potentials Workshop 2021
Commits
c5fbee0c
Commit
c5fbee0c
authored
4 years ago
by
Jan Janssen
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day_3/RuNNerMD.ipynb
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c5fbee0c
...
@@ -37,7 +37,7 @@
...
@@ -37,7 +37,7 @@
"metadata": {},
"metadata": {},
"outputs": [],
"outputs": [],
"source": [
"source": [
"j.potential = Project('../day_2/runner/runner_fit').load('fit').lammps_potential"
"j.potential = Project('../day_2/
02-
runner/runner_fit').load('fit').lammps_potential"
]
]
},
},
{
{
...
...
%% Cell type:code id:suffering-touch tags:
%% Cell type:code id:suffering-touch tags:
```
python
```
python
from
pyiron
import
Project
from
pyiron
import
Project
```
```
%% Cell type:code id:geological-bankruptcy tags:
%% Cell type:code id:geological-bankruptcy tags:
```
python
```
python
pr
=
Project
(
'
md_run
'
)
pr
=
Project
(
'
md_run
'
)
```
```
%% Cell type:code id:prompt-evaluation tags:
%% Cell type:code id:prompt-evaluation tags:
```
python
```
python
j
=
pr
.
create
.
job
.
Lammps
(
"
md
"
,
delete_existing_job
=
True
)
j
=
pr
.
create
.
job
.
Lammps
(
"
md
"
,
delete_existing_job
=
True
)
```
```
%% Cell type:code id:governing-consortium tags:
%% Cell type:code id:governing-consortium tags:
```
python
```
python
j
.
potential
=
Project
(
'
../day_2/runner/runner_fit
'
).
load
(
'
fit
'
).
lammps_potential
j
.
potential
=
Project
(
'
../day_2/
02-
runner/runner_fit
'
).
load
(
'
fit
'
).
lammps_potential
```
```
%% Cell type:code id:authentic-moscow tags:
%% Cell type:code id:authentic-moscow tags:
```
python
```
python
j
.
structure
=
pr
.
create
.
structure
.
ase_bulk
(
'
Cu
'
,
cubic
=
True
).
repeat
(
3
)
j
.
structure
=
pr
.
create
.
structure
.
ase_bulk
(
'
Cu
'
,
cubic
=
True
).
repeat
(
3
)
```
```
%% Cell type:code id:tamil-witch tags:
%% Cell type:code id:tamil-witch tags:
```
python
```
python
j
.
structure
.
plot3d
()
j
.
structure
.
plot3d
()
```
```
%% Output
%% Output
%% Cell type:code id:fatty-asbestos tags:
%% Cell type:code id:fatty-asbestos tags:
```
python
```
python
j
.
calc_md
(
n_ionic_steps
=
1000
,
temperature
=
500
)
j
.
calc_md
(
n_ionic_steps
=
1000
,
temperature
=
500
)
```
```
%% Cell type:code id:under-shirt tags:
%% Cell type:code id:under-shirt tags:
```
python
```
python
%%
time
%%
time
j
.
run
()
j
.
run
()
```
```
%% Output
%% Output
The job md was saved and received the ID: 13792062
The job md was saved and received the ID: 13792062
CPU times: user 370 ms, sys: 58 ms, total: 428 ms
CPU times: user 370 ms, sys: 58 ms, total: 428 ms
Wall time: 53 s
Wall time: 53 s
%% Cell type:code id:liked-thomson tags:
%% Cell type:code id:liked-thomson tags:
```
python
```
python
j
.
animate_structure
()
j
.
animate_structure
()
```
```
%% Output
%% Output
...
...
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