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Water interactive fix #366

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merged 3 commits into from
Sep 24, 2021
Merged

Water interactive fix #366

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9dbb211
Setting a dummy kspace style for compatibility
sudarsan-surendralal Sep 23, 2021
5d8c859
Update notebook
sudarsan-surendralal Sep 23, 2021
f4e2ae5
Merge pull request #368 from pyiron/master
jan-janssen Sep 24, 2021
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15 changes: 9 additions & 6 deletions notebooks/integration/interactive_units.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,8 @@
"outputs": [],
"source": [
"from pyiron_atomistics import Project\n",
"import numpy as np"
"import numpy as np\n",
"import pandas"
]
},
{
Expand Down Expand Up @@ -49,7 +50,8 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 4,
"id": "8589ee0f",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -64,7 +66,7 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": 5,
"id": "b42a1310",
"metadata": {},
"outputs": [
Expand All @@ -80,7 +82,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"The job test was saved and received the ID: 15620652\n"
"The job test was saved and received the ID: 15925922\n"
]
}
],
Expand All @@ -90,6 +92,7 @@
"job_int.structure = water\n",
"job_int.potential = water_potential\n",
"job_int.interactive_open()\n",
"job_int.interactive_water_bonds = True\n",
"job_int.calc_static()\n",
"job_int.run()\n",
"job_int.interactive_close()"
Expand All @@ -105,7 +108,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"The job test_ni was saved and received the ID: 15620654\n"
"The job test_ni was saved and received the ID: 15925923\n"
]
}
],
Expand Down Expand Up @@ -155,7 +158,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "c2cba1b5",
"id": "ae9d3022-35e0-4a29-ac87-fcac153a8e65",
"metadata": {},
"outputs": [],
"source": []
Expand Down
1 change: 1 addition & 0 deletions pyiron_atomistics/lammps/interactive.py
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Original file line number Diff line number Diff line change
Expand Up @@ -500,6 +500,7 @@ def _interactive_water_setter(self):
self._interactive_lib_command(group_h1)
self._interactive_lib_command(group_h2)
# A dummy pair style that does not have any Coulombic interactions needs to be initialized to create the bonds
self._interactive_lib_command("kspace_style none")
self._interactive_lib_command("pair_style lj/cut 2.5")
self._interactive_lib_command("pair_coeff * * 0.0 0.0")
self._interactive_lib_command("create_bonds many Oatoms H1atoms 1 0.7 1.4")
Expand Down