Spaces:
Running
Running
add mrore/update diatomics curves
Browse files
mlip_arena/tasks/combustion/water.ipynb
CHANGED
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@@ -34,10 +34,11 @@
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{
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"cell_type": "markdown",
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"metadata": {
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"tags": []
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"source": [
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{
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"source ~/.bashrc\n",
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"module load python\n",
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"source activate /pscratch/sd/c/cyrusyc/.conda/mlip-arena\n",
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"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/bin/python -m distributed.cli.dask_worker tcp://128.55.64.
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"\n"
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},
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/distributed/node.py:
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"Perhaps you already have a cluster running?\n",
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"Hosting the HTTP server on port
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" warnings.warn(\n"
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},
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"outputs": [
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"output_type": "error",
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"traceback": [
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"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
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-
"\u001b[0;
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"Cell \u001b[0;32mIn[5], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m results \u001b[38;5;241m=\u001b[39m \u001b[43mcombustion\u001b[49m\u001b[43m(\u001b[49m\u001b[43matoms\u001b[49m\u001b[43m)\u001b[49m\n",
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"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/flows.py:
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"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/flow_engine.py:
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"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/flow_engine.py:
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"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/
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"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/flow_engine.py:
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"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/
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"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/flow_engine.py:
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"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/
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"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/
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"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/
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"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/
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"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/
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"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/
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]
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}
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],
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.11.
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},
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"widgets": {
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"application/vnd.jupyter.widget-state+json": {
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{
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"cell_type": "markdown",
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"metadata": {
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"jp-MarkdownHeadingCollapsed": true,
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"tags": []
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},
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"source": [
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"## Intial configuration"
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]
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},
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{
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"source ~/.bashrc\n",
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"module load python\n",
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"source activate /pscratch/sd/c/cyrusyc/.conda/mlip-arena\n",
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"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/bin/python -m distributed.cli.dask_worker tcp://128.55.64.15:38781 --name dummy-name --nthreads 1 --memory-limit 59.60GiB --nanny --death-timeout 86400\n",
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"\n"
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]
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},
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/distributed/node.py:187: UserWarning: Port 8787 is already in use.\n",
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"Perhaps you already have a cluster running?\n",
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"Hosting the HTTP server on port 44831 instead\n",
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" warnings.warn(\n"
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]
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}
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},
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"outputs": [
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{
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"data": {
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"text/html": [
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"<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">12:01:53.150 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | prefect.engine - Created flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'khaki-hippo'</span> for flow<span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\"> 'combustion'</span>\n",
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"</pre>\n"
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],
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"text/plain": [
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"12:01:53.150 | \u001b[36mINFO\u001b[0m | prefect.engine - Created flow run\u001b[35m 'khaki-hippo'\u001b[0m for flow\u001b[1;35m 'combustion'\u001b[0m\n"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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},
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{
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"data": {
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"text/html": [
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"<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">12:01:53.156 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | prefect.engine - View at <span style=\"color: #0000ff; text-decoration-color: #0000ff\">https://app.prefect.cloud/account/f7d40474-9362-4bfa-8950-ee6a43ec00f3/workspace/d4bb0913-5f5e-49f7-bfc5-06509088baeb/runs/flow-run/ce836160-4f0d-49a4-90d8-227225cb8f4c</span>\n",
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"</pre>\n"
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],
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"text/plain": [
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"12:01:53.156 | \u001b[36mINFO\u001b[0m | prefect.engine - View at \u001b[94mhttps://app.prefect.cloud/account/f7d40474-9362-4bfa-8950-ee6a43ec00f3/workspace/d4bb0913-5f5e-49f7-bfc5-06509088baeb/runs/flow-run/ce836160-4f0d-49a4-90d8-227225cb8f4c\u001b[0m\n"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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},
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{
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"data": {
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"text/html": [
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"<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">12:01:53.523 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | prefect.task_runner.dask - Connecting to existing Dask cluster SLURMCluster(99282258, 'tcp://128.55.64.15:38781', workers=0, threads=0, memory=0 B)\n",
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"</pre>\n"
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],
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"text/plain": [
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"12:01:53.523 | \u001b[36mINFO\u001b[0m | prefect.task_runner.dask - Connecting to existing Dask cluster SLURMCluster(99282258, 'tcp://128.55.64.15:38781', workers=0, threads=0, memory=0 B)\n"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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},
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{
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"data": {
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"text/html": [
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"<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">13:06:57.332 | <span style=\"color: #d70000; text-decoration-color: #d70000\">ERROR</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'khaki-hippo'</span> - Encountered exception during execution: IndexError('too many indices for tensor of dimension 1')\n",
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| 329 |
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"Traceback (most recent call last):\n",
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| 330 |
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" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/flow_engine.py\", line 652, in run_context\n",
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" yield self\n",
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" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/flow_engine.py\", line 696, in run_flow_sync\n",
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" engine.call_flow_fn()\n",
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" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/flow_engine.py\", line 675, in call_flow_fn\n",
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" result = call_with_parameters(self.flow.fn, self.parameters)\n",
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" ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
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" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/utilities/callables.py\", line 206, in call_with_parameters\n",
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" return fn(*args, **kwargs)\n",
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" ^^^^^^^^^^^^^^^^^^^\n",
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" File \"/tmp/ipykernel_1849247/2043615938.py\", line 26, in combustion\n",
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" return [future.result() for future in futures]\n",
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" ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
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" File \"/tmp/ipykernel_1849247/2043615938.py\", line 26, in <listcomp>\n",
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" return [future.result() for future in futures]\n",
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" ^^^^^^^^^^^^^^^\n",
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" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect_dask/task_runners.py\", line 143, in result\n",
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" _result = self._final_state.result(\n",
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" ^^^^^^^^^^^^^^^^^^^^^^^^^\n",
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" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/client/schemas/objects.py\", line 314, in result\n",
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" return get_state_result(\n",
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" ^^^^^^^^^^^^^^^^^\n",
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" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/states.py\", line 75, in get_state_result\n",
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" return _get_state_result(\n",
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" ^^^^^^^^^^^^^^^^^^\n",
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" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/utilities/asyncutils.py\", line 399, in coroutine_wrapper\n",
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" return run_coro_as_sync(ctx_call())\n",
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" ^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
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" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/utilities/asyncutils.py\", line 243, in run_coro_as_sync\n",
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" return call.result()\n",
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" ^^^^^^^^^^^^^\n",
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" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/_internal/concurrency/calls.py\", line 312, in result\n",
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" return self.future.result(timeout=timeout)\n",
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" ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
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" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/_internal/concurrency/calls.py\", line 182, in result\n",
|
| 365 |
+
" return self.__get_result()\n",
|
| 366 |
+
" ^^^^^^^^^^^^^^^^^^^\n",
|
| 367 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/concurrent/futures/_base.py\", line 401, in __get_result\n",
|
| 368 |
+
" raise self._exception\n",
|
| 369 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/_internal/concurrency/calls.py\", line 383, in _run_async\n",
|
| 370 |
+
" result = await coro\n",
|
| 371 |
+
" ^^^^^^^^^^\n",
|
| 372 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/utilities/asyncutils.py\", line 225, in coroutine_wrapper\n",
|
| 373 |
+
" return await task\n",
|
| 374 |
+
" ^^^^^^^^^^\n",
|
| 375 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/utilities/asyncutils.py\", line 389, in ctx_call\n",
|
| 376 |
+
" result = await async_fn(*args, **kwargs)\n",
|
| 377 |
+
" ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
|
| 378 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/states.py\", line 138, in _get_state_result\n",
|
| 379 |
+
" raise await get_state_exception(state)\n",
|
| 380 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/task_engine.py\", line 763, in run_context\n",
|
| 381 |
+
" yield self\n",
|
| 382 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/task_engine.py\", line 1323, in run_task_sync\n",
|
| 383 |
+
" engine.call_task_fn(txn)\n",
|
| 384 |
+
" ^^^^^^^^^^^^^^^^^\n",
|
| 385 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/task_engine.py\", line 786, in call_task_fn\n",
|
| 386 |
+
" result = call_with_parameters(self.task.fn, parameters)\n",
|
| 387 |
+
" ^^^^^^^^^^^^^^^^^\n",
|
| 388 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/utilities/callables.py\", line 206, in call_with_parameters\n",
|
| 389 |
+
" return fn(*args, **kwargs)\n",
|
| 390 |
+
" ^^^^^^^^^^^^^^^^^\n",
|
| 391 |
+
" File \"/pscratch/sd/c/cyrusyc/mlip-arena/mlip_arena/tasks/md.py\", line 363, in run\n",
|
| 392 |
+
" md_runner.run(steps=n_steps)\n",
|
| 393 |
+
" ^^^^^^^^^^^^^^^^^\n",
|
| 394 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/ase/md/npt.py\", line 277, in run\n",
|
| 395 |
+
" self.initialize()\n",
|
| 396 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/ase/md/npt.py\", line 399, in initialize\n",
|
| 397 |
+
" self._calculate_q_past_and_future()\n",
|
| 398 |
+
" ^^^^^^^^^^^^^^^^^\n",
|
| 399 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/ase/md/npt.py\", line 608, in _calculate_q_past_and_future\n",
|
| 400 |
+
" self._calculate_q_future(self.atoms.get_forces(md=True))\n",
|
| 401 |
+
" ^^^^^^^^^^^^^^^^^\n",
|
| 402 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/ase/atoms.py\", line 812, in get_forces\n",
|
| 403 |
+
" forces = self._calc.get_forces(self)\n",
|
| 404 |
+
" ^^^^^^^^^^^^^^^^^\n",
|
| 405 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/ase/calculators/abc.py\", line 30, in get_forces\n",
|
| 406 |
+
" return self.get_property('forces', atoms)\n",
|
| 407 |
+
" ^^^^^^^^^^^^^^^^^\n",
|
| 408 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/ase/calculators/calculator.py\", line 538, in get_property\n",
|
| 409 |
+
" self.calculate(atoms, [name], system_changes)\n",
|
| 410 |
+
" ^^^^^^^^^^^^^^^^^\n",
|
| 411 |
+
" File \"/pscratch/sd/c/cyrusyc/mlip-arena/mlip_arena/models/externals/chgnet.py\", line 36, in calculate\n",
|
| 412 |
+
" super().calculate(atoms, properties, system_changes)\n",
|
| 413 |
+
" ^^^^^^^^^^^^^^^^^\n",
|
| 414 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/chgnet/model/dynamics.py\", line 143, in calculate\n",
|
| 415 |
+
" model_prediction = self.model.predict_graph(\n",
|
| 416 |
+
" ^^^^^^^^^^^^^^^^^\n",
|
| 417 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/chgnet/model/model.py\", line 627, in predict_graph\n",
|
| 418 |
+
" prediction = self.forward(\n",
|
| 419 |
+
" ^^^^^^^^^^^^^^^^^\n",
|
| 420 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/chgnet/model/model.py\", line 359, in forward\n",
|
| 421 |
+
" batched_graph = BatchedGraph.from_graphs(\n",
|
| 422 |
+
" ^^^^^^^^^^^^^^^^^\n",
|
| 423 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/chgnet/model/model.py\", line 822, in from_graphs\n",
|
| 424 |
+
" center=atom_cart_coords[graph.atom_graph[:, 0]],\n",
|
| 425 |
+
" ^^^^^^^^^^^^^^^^^\n",
|
| 426 |
+
"IndexError: too many indices for tensor of dimension 1\n",
|
| 427 |
+
"</pre>\n"
|
| 428 |
+
],
|
| 429 |
+
"text/plain": [
|
| 430 |
+
"13:06:57.332 | \u001b[38;5;160mERROR\u001b[0m | Flow run\u001b[35m 'khaki-hippo'\u001b[0m - Encountered exception during execution: IndexError('too many indices for tensor of dimension 1')\n",
|
| 431 |
+
"Traceback (most recent call last):\n",
|
| 432 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/flow_engine.py\", line 652, in run_context\n",
|
| 433 |
+
" yield self\n",
|
| 434 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/flow_engine.py\", line 696, in run_flow_sync\n",
|
| 435 |
+
" engine.call_flow_fn()\n",
|
| 436 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/flow_engine.py\", line 675, in call_flow_fn\n",
|
| 437 |
+
" result = call_with_parameters(self.flow.fn, self.parameters)\n",
|
| 438 |
+
" ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
|
| 439 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/utilities/callables.py\", line 206, in call_with_parameters\n",
|
| 440 |
+
" return fn(*args, **kwargs)\n",
|
| 441 |
+
" ^^^^^^^^^^^^^^^^^^^\n",
|
| 442 |
+
" File \"/tmp/ipykernel_1849247/2043615938.py\", line 26, in combustion\n",
|
| 443 |
+
" return [future.result() for future in futures]\n",
|
| 444 |
+
" ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
|
| 445 |
+
" File \"/tmp/ipykernel_1849247/2043615938.py\", line 26, in <listcomp>\n",
|
| 446 |
+
" return [future.result() for future in futures]\n",
|
| 447 |
+
" ^^^^^^^^^^^^^^^\n",
|
| 448 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect_dask/task_runners.py\", line 143, in result\n",
|
| 449 |
+
" _result = self._final_state.result(\n",
|
| 450 |
+
" ^^^^^^^^^^^^^^^^^^^^^^^^^\n",
|
| 451 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/client/schemas/objects.py\", line 314, in result\n",
|
| 452 |
+
" return get_state_result(\n",
|
| 453 |
+
" ^^^^^^^^^^^^^^^^^\n",
|
| 454 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/states.py\", line 75, in get_state_result\n",
|
| 455 |
+
" return _get_state_result(\n",
|
| 456 |
+
" ^^^^^^^^^^^^^^^^^^\n",
|
| 457 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/utilities/asyncutils.py\", line 399, in coroutine_wrapper\n",
|
| 458 |
+
" return run_coro_as_sync(ctx_call())\n",
|
| 459 |
+
" ^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
|
| 460 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/utilities/asyncutils.py\", line 243, in run_coro_as_sync\n",
|
| 461 |
+
" return call.result()\n",
|
| 462 |
+
" ^^^^^^^^^^^^^\n",
|
| 463 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/_internal/concurrency/calls.py\", line 312, in result\n",
|
| 464 |
+
" return self.future.result(timeout=timeout)\n",
|
| 465 |
+
" ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
|
| 466 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/_internal/concurrency/calls.py\", line 182, in result\n",
|
| 467 |
+
" return self.__get_result()\n",
|
| 468 |
+
" ^^^^^^^^^^^^^^^^^^^\n",
|
| 469 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/concurrent/futures/_base.py\", line 401, in __get_result\n",
|
| 470 |
+
" raise self._exception\n",
|
| 471 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/_internal/concurrency/calls.py\", line 383, in _run_async\n",
|
| 472 |
+
" result = await coro\n",
|
| 473 |
+
" ^^^^^^^^^^\n",
|
| 474 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/utilities/asyncutils.py\", line 225, in coroutine_wrapper\n",
|
| 475 |
+
" return await task\n",
|
| 476 |
+
" ^^^^^^^^^^\n",
|
| 477 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/utilities/asyncutils.py\", line 389, in ctx_call\n",
|
| 478 |
+
" result = await async_fn(*args, **kwargs)\n",
|
| 479 |
+
" ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
|
| 480 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/states.py\", line 138, in _get_state_result\n",
|
| 481 |
+
" raise await get_state_exception(state)\n",
|
| 482 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/task_engine.py\", line 763, in run_context\n",
|
| 483 |
+
" yield self\n",
|
| 484 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/task_engine.py\", line 1323, in run_task_sync\n",
|
| 485 |
+
" engine.call_task_fn(txn)\n",
|
| 486 |
+
" ^^^^^^^^^^^^^^^^^\n",
|
| 487 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/task_engine.py\", line 786, in call_task_fn\n",
|
| 488 |
+
" result = call_with_parameters(self.task.fn, parameters)\n",
|
| 489 |
+
" ^^^^^^^^^^^^^^^^^\n",
|
| 490 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/utilities/callables.py\", line 206, in call_with_parameters\n",
|
| 491 |
+
" return fn(*args, **kwargs)\n",
|
| 492 |
+
" ^^^^^^^^^^^^^^^^^\n",
|
| 493 |
+
" File \"/pscratch/sd/c/cyrusyc/mlip-arena/mlip_arena/tasks/md.py\", line 363, in run\n",
|
| 494 |
+
" md_runner.run(steps=n_steps)\n",
|
| 495 |
+
" ^^^^^^^^^^^^^^^^^\n",
|
| 496 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/ase/md/npt.py\", line 277, in run\n",
|
| 497 |
+
" self.initialize()\n",
|
| 498 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/ase/md/npt.py\", line 399, in initialize\n",
|
| 499 |
+
" self._calculate_q_past_and_future()\n",
|
| 500 |
+
" ^^^^^^^^^^^^^^^^^\n",
|
| 501 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/ase/md/npt.py\", line 608, in _calculate_q_past_and_future\n",
|
| 502 |
+
" self._calculate_q_future(self.atoms.get_forces(md=True))\n",
|
| 503 |
+
" ^^^^^^^^^^^^^^^^^\n",
|
| 504 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/ase/atoms.py\", line 812, in get_forces\n",
|
| 505 |
+
" forces = self._calc.get_forces(self)\n",
|
| 506 |
+
" ^^^^^^^^^^^^^^^^^\n",
|
| 507 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/ase/calculators/abc.py\", line 30, in get_forces\n",
|
| 508 |
+
" return self.get_property('forces', atoms)\n",
|
| 509 |
+
" ^^^^^^^^^^^^^^^^^\n",
|
| 510 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/ase/calculators/calculator.py\", line 538, in get_property\n",
|
| 511 |
+
" self.calculate(atoms, [name], system_changes)\n",
|
| 512 |
+
" ^^^^^^^^^^^^^^^^^\n",
|
| 513 |
+
" File \"/pscratch/sd/c/cyrusyc/mlip-arena/mlip_arena/models/externals/chgnet.py\", line 36, in calculate\n",
|
| 514 |
+
" super().calculate(atoms, properties, system_changes)\n",
|
| 515 |
+
" ^^^^^^^^^^^^^^^^^\n",
|
| 516 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/chgnet/model/dynamics.py\", line 143, in calculate\n",
|
| 517 |
+
" model_prediction = self.model.predict_graph(\n",
|
| 518 |
+
" ^^^^^^^^^^^^^^^^^\n",
|
| 519 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/chgnet/model/model.py\", line 627, in predict_graph\n",
|
| 520 |
+
" prediction = self.forward(\n",
|
| 521 |
+
" ^^^^^^^^^^^^^^^^^\n",
|
| 522 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/chgnet/model/model.py\", line 359, in forward\n",
|
| 523 |
+
" batched_graph = BatchedGraph.from_graphs(\n",
|
| 524 |
+
" ^^^^^^^^^^^^^^^^^\n",
|
| 525 |
+
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/chgnet/model/model.py\", line 822, in from_graphs\n",
|
| 526 |
+
" center=atom_cart_coords[graph.atom_graph[:, 0]],\n",
|
| 527 |
+
" ^^^^^^^^^^^^^^^^^\n",
|
| 528 |
+
"IndexError: too many indices for tensor of dimension 1\n"
|
| 529 |
+
]
|
| 530 |
+
},
|
| 531 |
+
"metadata": {},
|
| 532 |
+
"output_type": "display_data"
|
| 533 |
+
},
|
| 534 |
+
{
|
| 535 |
+
"data": {
|
| 536 |
+
"text/html": [
|
| 537 |
+
"<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">13:06:58.009 | <span style=\"color: #d70000; text-decoration-color: #d70000\">ERROR</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'khaki-hippo'</span> - Finished in state <span style=\"color: #d70000; text-decoration-color: #d70000\">Failed</span>('Flow run encountered an exception: IndexError: too many indices for tensor of dimension 1')\n",
|
| 538 |
+
"</pre>\n"
|
| 539 |
+
],
|
| 540 |
+
"text/plain": [
|
| 541 |
+
"13:06:58.009 | \u001b[38;5;160mERROR\u001b[0m | Flow run\u001b[35m 'khaki-hippo'\u001b[0m - Finished in state \u001b[38;5;160mFailed\u001b[0m('Flow run encountered an exception: IndexError: too many indices for tensor of dimension 1')\n"
|
| 542 |
+
]
|
| 543 |
+
},
|
| 544 |
+
"metadata": {},
|
| 545 |
+
"output_type": "display_data"
|
| 546 |
+
},
|
| 547 |
+
{
|
| 548 |
+
"ename": "IndexError",
|
| 549 |
+
"evalue": "too many indices for tensor of dimension 1",
|
| 550 |
"output_type": "error",
|
| 551 |
"traceback": [
|
| 552 |
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
|
| 553 |
+
"\u001b[0;31mIndexError\u001b[0m Traceback (most recent call last)",
|
| 554 |
"Cell \u001b[0;32mIn[5], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m results \u001b[38;5;241m=\u001b[39m \u001b[43mcombustion\u001b[49m\u001b[43m(\u001b[49m\u001b[43matoms\u001b[49m\u001b[43m)\u001b[49m\n",
|
| 555 |
+
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/flows.py:1345\u001b[0m, in \u001b[0;36mFlow.__call__\u001b[0;34m(self, return_state, wait_for, *args, **kwargs)\u001b[0m\n\u001b[1;32m 1341\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m track_viz_task(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39misasync, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mname, parameters)\n\u001b[1;32m 1343\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mprefect\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mflow_engine\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m run_flow\n\u001b[0;32m-> 1345\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mrun_flow\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 1346\u001b[0m \u001b[43m \u001b[49m\u001b[43mflow\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1347\u001b[0m \u001b[43m \u001b[49m\u001b[43mparameters\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mparameters\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1348\u001b[0m \u001b[43m \u001b[49m\u001b[43mwait_for\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mwait_for\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1349\u001b[0m \u001b[43m \u001b[49m\u001b[43mreturn_type\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mreturn_type\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1350\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n",
|
| 556 |
+
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/flow_engine.py:818\u001b[0m, in \u001b[0;36mrun_flow\u001b[0;34m(flow, flow_run, parameters, wait_for, return_type)\u001b[0m\n\u001b[1;32m 816\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m run_flow_async(\u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m 817\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 818\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mrun_flow_sync\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n",
|
| 557 |
+
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/flow_engine.py:698\u001b[0m, in \u001b[0;36mrun_flow_sync\u001b[0;34m(flow, flow_run, parameters, wait_for, return_type)\u001b[0m\n\u001b[1;32m 695\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m engine\u001b[38;5;241m.\u001b[39mrun_context():\n\u001b[1;32m 696\u001b[0m engine\u001b[38;5;241m.\u001b[39mcall_flow_fn()\n\u001b[0;32m--> 698\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m engine\u001b[38;5;241m.\u001b[39mstate \u001b[38;5;28;01mif\u001b[39;00m return_type \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mstate\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;28;01melse\u001b[39;00m \u001b[43mengine\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mresult\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n",
|
| 558 |
+
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/flow_engine.py:255\u001b[0m, in \u001b[0;36mFlowRunEngine.result\u001b[0;34m(self, raise_on_failure)\u001b[0m\n\u001b[1;32m 253\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_raised \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m NotSet:\n\u001b[1;32m 254\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m raise_on_failure:\n\u001b[0;32m--> 255\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_raised\n\u001b[1;32m 256\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_raised\n\u001b[1;32m 258\u001b[0m \u001b[38;5;66;03m# This is a fall through case which leans on the existing state result mechanics to get the\u001b[39;00m\n\u001b[1;32m 259\u001b[0m \u001b[38;5;66;03m# return value. This is necessary because we currently will return a State object if the\u001b[39;00m\n\u001b[1;32m 260\u001b[0m \u001b[38;5;66;03m# the State was Prefect-created.\u001b[39;00m\n\u001b[1;32m 261\u001b[0m \u001b[38;5;66;03m# TODO: Remove the need to get the result from a State except in cases where the return value\u001b[39;00m\n\u001b[1;32m 262\u001b[0m \u001b[38;5;66;03m# is a State object.\u001b[39;00m\n",
|
| 559 |
+
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/flow_engine.py:652\u001b[0m, in \u001b[0;36mFlowRunEngine.run_context\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 645\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m timeout_context(\n\u001b[1;32m 646\u001b[0m seconds\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mflow\u001b[38;5;241m.\u001b[39mtimeout_seconds,\n\u001b[1;32m 647\u001b[0m timeout_exc_type\u001b[38;5;241m=\u001b[39mFlowRunTimeoutError,\n\u001b[1;32m 648\u001b[0m ):\n\u001b[1;32m 649\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mlogger\u001b[38;5;241m.\u001b[39mdebug(\n\u001b[1;32m 650\u001b[0m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mExecuting flow \u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mflow\u001b[38;5;241m.\u001b[39mname\u001b[38;5;132;01m!r}\u001b[39;00m\u001b[38;5;124m for flow run \u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mflow_run\u001b[38;5;241m.\u001b[39mname\u001b[38;5;132;01m!r}\u001b[39;00m\u001b[38;5;124m...\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 651\u001b[0m )\n\u001b[0;32m--> 652\u001b[0m \u001b[38;5;28;01myield\u001b[39;00m \u001b[38;5;28mself\u001b[39m\n\u001b[1;32m 653\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mTimeoutError\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m exc:\n\u001b[1;32m 654\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mhandle_timeout(exc)\n",
|
| 560 |
+
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/flow_engine.py:696\u001b[0m, in \u001b[0;36mrun_flow_sync\u001b[0;34m(flow, flow_run, parameters, wait_for, return_type)\u001b[0m\n\u001b[1;32m 694\u001b[0m \u001b[38;5;28;01mwhile\u001b[39;00m engine\u001b[38;5;241m.\u001b[39mis_running():\n\u001b[1;32m 695\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m engine\u001b[38;5;241m.\u001b[39mrun_context():\n\u001b[0;32m--> 696\u001b[0m \u001b[43mengine\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcall_flow_fn\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 698\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m engine\u001b[38;5;241m.\u001b[39mstate \u001b[38;5;28;01mif\u001b[39;00m return_type \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mstate\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;28;01melse\u001b[39;00m engine\u001b[38;5;241m.\u001b[39mresult()\n",
|
| 561 |
+
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/flow_engine.py:675\u001b[0m, in \u001b[0;36mFlowRunEngine.call_flow_fn\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 673\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m _call_flow_fn()\n\u001b[1;32m 674\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 675\u001b[0m result \u001b[38;5;241m=\u001b[39m \u001b[43mcall_with_parameters\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mflow\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mfn\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mparameters\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 676\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mhandle_success(result)\n",
|
| 562 |
+
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/utilities/callables.py:206\u001b[0m, in \u001b[0;36mcall_with_parameters\u001b[0;34m(fn, parameters)\u001b[0m\n\u001b[1;32m 198\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 199\u001b[0m \u001b[38;5;124;03mCall a function with parameters extracted with `get_call_parameters`\u001b[39;00m\n\u001b[1;32m 200\u001b[0m \n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 203\u001b[0m \u001b[38;5;124;03mthe args/kwargs using `parameters_to_positional_and_keyword` directly\u001b[39;00m\n\u001b[1;32m 204\u001b[0m \u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 205\u001b[0m args, kwargs \u001b[38;5;241m=\u001b[39m parameters_to_args_kwargs(fn, parameters)\n\u001b[0;32m--> 206\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mfn\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n",
|
| 563 |
+
"Cell \u001b[0;32mIn[4], line 26\u001b[0m, in \u001b[0;36mcombustion\u001b[0;34m(atoms)\u001b[0m\n\u001b[1;32m 6\u001b[0m future \u001b[38;5;241m=\u001b[39m MD\u001b[38;5;241m.\u001b[39msubmit(\n\u001b[1;32m 7\u001b[0m atoms\u001b[38;5;241m=\u001b[39matoms,\n\u001b[1;32m 8\u001b[0m calculator_name\u001b[38;5;241m=\u001b[39mmodel,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 21\u001b[0m restart\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m,\n\u001b[1;32m 22\u001b[0m )\n\u001b[1;32m 24\u001b[0m futures\u001b[38;5;241m.\u001b[39mappend(future)\n\u001b[0;32m---> 26\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43m[\u001b[49m\u001b[43mfuture\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mresult\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mfor\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[43mfuture\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;129;43;01min\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[43mfutures\u001b[49m\u001b[43m]\u001b[49m\n",
|
| 564 |
+
"Cell \u001b[0;32mIn[4], line 26\u001b[0m, in \u001b[0;36m<listcomp>\u001b[0;34m(.0)\u001b[0m\n\u001b[1;32m 6\u001b[0m future \u001b[38;5;241m=\u001b[39m MD\u001b[38;5;241m.\u001b[39msubmit(\n\u001b[1;32m 7\u001b[0m atoms\u001b[38;5;241m=\u001b[39matoms,\n\u001b[1;32m 8\u001b[0m calculator_name\u001b[38;5;241m=\u001b[39mmodel,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 21\u001b[0m restart\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m,\n\u001b[1;32m 22\u001b[0m )\n\u001b[1;32m 24\u001b[0m futures\u001b[38;5;241m.\u001b[39mappend(future)\n\u001b[0;32m---> 26\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m [\u001b[43mfuture\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mresult\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m \u001b[38;5;28;01mfor\u001b[39;00m future \u001b[38;5;129;01min\u001b[39;00m futures]\n",
|
| 565 |
+
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect_dask/task_runners.py:143\u001b[0m, in \u001b[0;36mPrefectDaskFuture.result\u001b[0;34m(self, timeout, raise_on_failure)\u001b[0m\n\u001b[1;32m 140\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 141\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m future_result\n\u001b[0;32m--> 143\u001b[0m _result \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_final_state\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mresult\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 144\u001b[0m \u001b[43m \u001b[49m\u001b[43mraise_on_failure\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mraise_on_failure\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfetch\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\n\u001b[1;32m 145\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 146\u001b[0m \u001b[38;5;66;03m# state.result is a `sync_compatible` function that may or may not return an awaitable\u001b[39;00m\n\u001b[1;32m 147\u001b[0m \u001b[38;5;66;03m# depending on whether the parent frame is sync or not\u001b[39;00m\n\u001b[1;32m 148\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m asyncio\u001b[38;5;241m.\u001b[39miscoroutine(_result):\n",
|
| 566 |
+
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/client/schemas/objects.py:314\u001b[0m, in \u001b[0;36mState.result\u001b[0;34m(self, raise_on_failure, fetch, retry_result_failure)\u001b[0m\n\u001b[1;32m 229\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 230\u001b[0m \u001b[38;5;124;03mRetrieve the result attached to this state.\u001b[39;00m\n\u001b[1;32m 231\u001b[0m \n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 310\u001b[0m \u001b[38;5;124;03m >>> await flow_run.state.result(raise_on_failure=True, fetch=True) # Raises `ValueError(\"oh no!\")`\u001b[39;00m\n\u001b[1;32m 311\u001b[0m \u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 312\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mprefect\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mstates\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m get_state_result\n\u001b[0;32m--> 314\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mget_state_result\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 315\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 316\u001b[0m \u001b[43m \u001b[49m\u001b[43mraise_on_failure\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mraise_on_failure\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 317\u001b[0m \u001b[43m \u001b[49m\u001b[43mfetch\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mfetch\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 318\u001b[0m \u001b[43m \u001b[49m\u001b[43mretry_result_failure\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mretry_result_failure\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 319\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n",
|
| 567 |
+
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/states.py:75\u001b[0m, in \u001b[0;36mget_state_result\u001b[0;34m(state, raise_on_failure, fetch, retry_result_failure)\u001b[0m\n\u001b[1;32m 73\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m state\u001b[38;5;241m.\u001b[39mdata\n\u001b[1;32m 74\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m---> 75\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43m_get_state_result\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 76\u001b[0m \u001b[43m \u001b[49m\u001b[43mstate\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 77\u001b[0m \u001b[43m \u001b[49m\u001b[43mraise_on_failure\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mraise_on_failure\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 78\u001b[0m \u001b[43m \u001b[49m\u001b[43mretry_result_failure\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mretry_result_failure\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 79\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n",
|
| 568 |
+
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/utilities/asyncutils.py:399\u001b[0m, in \u001b[0;36msync_compatible.<locals>.coroutine_wrapper\u001b[0;34m(_sync, *args, **kwargs)\u001b[0m\n\u001b[1;32m 397\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m ctx_call()\n\u001b[1;32m 398\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 399\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mrun_coro_as_sync\u001b[49m\u001b[43m(\u001b[49m\u001b[43mctx_call\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[43m)\u001b[49m\n",
|
| 569 |
+
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/utilities/asyncutils.py:243\u001b[0m, in \u001b[0;36mrun_coro_as_sync\u001b[0;34m(coroutine, force_new_thread, wait_for_result)\u001b[0m\n\u001b[1;32m 241\u001b[0m runner\u001b[38;5;241m.\u001b[39msubmit(call)\n\u001b[1;32m 242\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 243\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mcall\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mresult\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 244\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyboardInterrupt\u001b[39;00m:\n\u001b[1;32m 245\u001b[0m call\u001b[38;5;241m.\u001b[39mcancel()\n",
|
| 570 |
+
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/_internal/concurrency/calls.py:312\u001b[0m, in \u001b[0;36mCall.result\u001b[0;34m(self, timeout)\u001b[0m\n\u001b[1;32m 306\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mresult\u001b[39m(\u001b[38;5;28mself\u001b[39m, timeout: Optional[\u001b[38;5;28mfloat\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m T:\n\u001b[1;32m 307\u001b[0m \u001b[38;5;250m \u001b[39m\u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 308\u001b[0m \u001b[38;5;124;03m Wait for the result of the call.\u001b[39;00m\n\u001b[1;32m 309\u001b[0m \n\u001b[1;32m 310\u001b[0m \u001b[38;5;124;03m Not safe for use from asynchronous contexts.\u001b[39;00m\n\u001b[1;32m 311\u001b[0m \u001b[38;5;124;03m \"\"\"\u001b[39;00m\n\u001b[0;32m--> 312\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mfuture\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mresult\u001b[49m\u001b[43m(\u001b[49m\u001b[43mtimeout\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mtimeout\u001b[49m\u001b[43m)\u001b[49m\n",
|
| 571 |
+
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/_internal/concurrency/calls.py:182\u001b[0m, in \u001b[0;36mFuture.result\u001b[0;34m(self, timeout)\u001b[0m\n\u001b[1;32m 180\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m CancelledError()\n\u001b[1;32m 181\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_state \u001b[38;5;241m==\u001b[39m FINISHED:\n\u001b[0;32m--> 182\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m__get_result\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 183\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 184\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mTimeoutError\u001b[39;00m()\n",
|
| 572 |
+
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/concurrent/futures/_base.py:401\u001b[0m, in \u001b[0;36mFuture.__get_result\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 399\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_exception:\n\u001b[1;32m 400\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 401\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_exception\n\u001b[1;32m 402\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m 403\u001b[0m \u001b[38;5;66;03m# Break a reference cycle with the exception in self._exception\u001b[39;00m\n\u001b[1;32m 404\u001b[0m \u001b[38;5;28mself\u001b[39m \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n",
|
| 573 |
+
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/_internal/concurrency/calls.py:383\u001b[0m, in \u001b[0;36mCall._run_async\u001b[0;34m(***failed resolving arguments***)\u001b[0m\n\u001b[1;32m 381\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mfuture\u001b[38;5;241m.\u001b[39menforce_async_deadline() \u001b[38;5;28;01mas\u001b[39;00m cancel_scope:\n\u001b[1;32m 382\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 383\u001b[0m result \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m coro\n\u001b[1;32m 384\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m 385\u001b[0m \u001b[38;5;66;03m# Forget this call's arguments in order to free up any memory\u001b[39;00m\n\u001b[1;32m 386\u001b[0m \u001b[38;5;66;03m# that may be referenced by them; after a call has happened,\u001b[39;00m\n\u001b[1;32m 387\u001b[0m \u001b[38;5;66;03m# there's no need to keep a reference to them\u001b[39;00m\n\u001b[1;32m 388\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39margs \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n",
|
| 574 |
+
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/utilities/asyncutils.py:225\u001b[0m, in \u001b[0;36mrun_coro_as_sync.<locals>.coroutine_wrapper\u001b[0;34m()\u001b[0m\n\u001b[1;32m 223\u001b[0m task \u001b[38;5;241m=\u001b[39m create_task(coroutine)\n\u001b[1;32m 224\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m wait_for_result:\n\u001b[0;32m--> 225\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;01mawait\u001b[39;00m task\n\u001b[1;32m 226\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m 227\u001b[0m RUNNING_IN_RUN_SYNC_LOOP_FLAG\u001b[38;5;241m.\u001b[39mreset(token1)\n",
|
| 575 |
+
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/utilities/asyncutils.py:389\u001b[0m, in \u001b[0;36msync_compatible.<locals>.coroutine_wrapper.<locals>.ctx_call\u001b[0;34m()\u001b[0m\n\u001b[1;32m 387\u001b[0m token \u001b[38;5;241m=\u001b[39m RUNNING_ASYNC_FLAG\u001b[38;5;241m.\u001b[39mset(\u001b[38;5;28;01mTrue\u001b[39;00m)\n\u001b[1;32m 388\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 389\u001b[0m result \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m async_fn(\u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m 390\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m 391\u001b[0m RUNNING_ASYNC_FLAG\u001b[38;5;241m.\u001b[39mreset(token)\n",
|
| 576 |
+
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/states.py:138\u001b[0m, in \u001b[0;36m_get_state_result\u001b[0;34m(state, raise_on_failure, retry_result_failure)\u001b[0m\n\u001b[1;32m 131\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m UnfinishedRun(\n\u001b[1;32m 132\u001b[0m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mRun is in \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mstate\u001b[38;5;241m.\u001b[39mtype\u001b[38;5;241m.\u001b[39mname\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m state, its result is not available.\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 133\u001b[0m )\n\u001b[1;32m 135\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m raise_on_failure \u001b[38;5;129;01mand\u001b[39;00m (\n\u001b[1;32m 136\u001b[0m state\u001b[38;5;241m.\u001b[39mis_crashed() \u001b[38;5;129;01mor\u001b[39;00m state\u001b[38;5;241m.\u001b[39mis_failed() \u001b[38;5;129;01mor\u001b[39;00m state\u001b[38;5;241m.\u001b[39mis_cancelled()\n\u001b[1;32m 137\u001b[0m ):\n\u001b[0;32m--> 138\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;28;01mawait\u001b[39;00m get_state_exception(state)\n\u001b[1;32m 140\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(state\u001b[38;5;241m.\u001b[39mdata, (BaseResult, ResultRecordMetadata)):\n\u001b[1;32m 141\u001b[0m result \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m _get_state_result_data_with_retries(\n\u001b[1;32m 142\u001b[0m state, retry_result_failure\u001b[38;5;241m=\u001b[39mretry_result_failure\n\u001b[1;32m 143\u001b[0m )\n",
|
| 577 |
+
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/task_engine.py:763\u001b[0m, in \u001b[0;36mrun_context\u001b[0;34m()\u001b[0m\n\u001b[1;32m 760\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mis_cancelled():\n\u001b[1;32m 761\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m CancelledError(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mTask run cancelled by the task runner\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m--> 763\u001b[0m \u001b[38;5;28;01myield\u001b[39;00m \u001b[38;5;28mself\u001b[39m\n\u001b[1;32m 764\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mTimeoutError\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m exc:\n\u001b[1;32m 765\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mhandle_timeout(exc)\n",
|
| 578 |
+
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/task_engine.py:1323\u001b[0m, in \u001b[0;36mrun_task_sync\u001b[0;34m()\u001b[0m\n\u001b[1;32m 1321\u001b[0m run_coro_as_sync(engine\u001b[38;5;241m.\u001b[39mwait_until_ready())\n\u001b[1;32m 1322\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m engine\u001b[38;5;241m.\u001b[39mrun_context(), engine\u001b[38;5;241m.\u001b[39mtransaction_context() \u001b[38;5;28;01mas\u001b[39;00m txn:\n\u001b[0;32m-> 1323\u001b[0m engine\u001b[38;5;241m.\u001b[39mcall_task_fn(txn)\n\u001b[1;32m 1325\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m engine\u001b[38;5;241m.\u001b[39mstate \u001b[38;5;28;01mif\u001b[39;00m return_type \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mstate\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;28;01melse\u001b[39;00m engine\u001b[38;5;241m.\u001b[39mresult()\n",
|
| 579 |
+
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/task_engine.py:786\u001b[0m, in \u001b[0;36mcall_task_fn\u001b[0;34m()\u001b[0m\n\u001b[1;32m 784\u001b[0m result \u001b[38;5;241m=\u001b[39m call_with_parameters(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mtask\u001b[38;5;241m.\u001b[39mfn, parameters)\n\u001b[1;32m 785\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 786\u001b[0m result \u001b[38;5;241m=\u001b[39m call_with_parameters(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mtask\u001b[38;5;241m.\u001b[39mfn, parameters)\n\u001b[1;32m 787\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mhandle_success(result, transaction\u001b[38;5;241m=\u001b[39mtransaction)\n\u001b[1;32m 788\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m result\n",
|
| 580 |
+
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/utilities/callables.py:206\u001b[0m, in \u001b[0;36mcall_with_parameters\u001b[0;34m()\u001b[0m\n\u001b[1;32m 198\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 199\u001b[0m \u001b[38;5;124;03mCall a function with parameters extracted with `get_call_parameters`\u001b[39;00m\n\u001b[1;32m 200\u001b[0m \n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 203\u001b[0m \u001b[38;5;124;03mthe args/kwargs using `parameters_to_positional_and_keyword` directly\u001b[39;00m\n\u001b[1;32m 204\u001b[0m \u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 205\u001b[0m args, kwargs \u001b[38;5;241m=\u001b[39m parameters_to_args_kwargs(fn, parameters)\n\u001b[0;32m--> 206\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m fn(\u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n",
|
| 581 |
+
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/mlip-arena/mlip_arena/tasks/md.py:363\u001b[0m, in \u001b[0;36mrun\u001b[0;34m()\u001b[0m\n\u001b[1;32m 360\u001b[0m md_runner\u001b[38;5;241m.\u001b[39mattach(_callback, interval\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m1\u001b[39m)\n\u001b[1;32m 362\u001b[0m start_time \u001b[38;5;241m=\u001b[39m datetime\u001b[38;5;241m.\u001b[39mnow()\n\u001b[0;32m--> 363\u001b[0m md_runner\u001b[38;5;241m.\u001b[39mrun(steps\u001b[38;5;241m=\u001b[39mn_steps)\n\u001b[1;32m 364\u001b[0m end_time \u001b[38;5;241m=\u001b[39m datetime\u001b[38;5;241m.\u001b[39mnow()\n\u001b[1;32m 366\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m traj_file \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n",
|
| 582 |
+
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/ase/md/npt.py:277\u001b[0m, in \u001b[0;36mrun\u001b[0;34m()\u001b[0m\n\u001b[1;32m 275\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\"Perform a number of time steps.\"\"\"\u001b[39;00m\n\u001b[1;32m 276\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39minitialized:\n\u001b[0;32m--> 277\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39minitialize()\n\u001b[1;32m 278\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 279\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mhave_the_atoms_been_changed():\n",
|
| 583 |
+
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/ase/md/npt.py:399\u001b[0m, in \u001b[0;36minitialize\u001b[0;34m()\u001b[0m\n\u001b[1;32m 396\u001b[0m deltazeta \u001b[38;5;241m=\u001b[39m dt \u001b[38;5;241m*\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mtfact \u001b[38;5;241m*\u001b[39m (atoms\u001b[38;5;241m.\u001b[39mget_kinetic_energy() \u001b[38;5;241m-\u001b[39m\n\u001b[1;32m 397\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdesiredEkin)\n\u001b[1;32m 398\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mzeta_past \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mzeta \u001b[38;5;241m-\u001b[39m deltazeta\n\u001b[0;32m--> 399\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_calculate_q_past_and_future()\n\u001b[1;32m 400\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39minitialized \u001b[38;5;241m=\u001b[39m \u001b[38;5;241m1\u001b[39m\n",
|
| 584 |
+
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/ase/md/npt.py:608\u001b[0m, in \u001b[0;36m_calculate_q_past_and_future\u001b[0;34m()\u001b[0m\n\u001b[1;32m 606\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m i \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mrange\u001b[39m(\u001b[38;5;241m2\u001b[39m):\n\u001b[1;32m 607\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mq_past \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mq \u001b[38;5;241m-\u001b[39m dt \u001b[38;5;241m*\u001b[39m np\u001b[38;5;241m.\u001b[39mdot(p \u001b[38;5;241m/\u001b[39m m, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39minv_h)\n\u001b[0;32m--> 608\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_calculate_q_future(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39matoms\u001b[38;5;241m.\u001b[39mget_forces(md\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m))\n\u001b[1;32m 609\u001b[0m p \u001b[38;5;241m=\u001b[39m np\u001b[38;5;241m.\u001b[39mdot(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mq_future \u001b[38;5;241m-\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mq_past, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mh \u001b[38;5;241m/\u001b[39m (\u001b[38;5;241m2\u001b[39m \u001b[38;5;241m*\u001b[39m dt)) \u001b[38;5;241m*\u001b[39m m\n\u001b[1;32m 610\u001b[0m e \u001b[38;5;241m=\u001b[39m ekin(p)\n",
|
| 585 |
+
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/ase/atoms.py:812\u001b[0m, in \u001b[0;36mget_forces\u001b[0;34m()\u001b[0m\n\u001b[1;32m 810\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_calc \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 811\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mRuntimeError\u001b[39;00m(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mAtoms object has no calculator.\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[0;32m--> 812\u001b[0m forces \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_calc\u001b[38;5;241m.\u001b[39mget_forces(\u001b[38;5;28mself\u001b[39m)\n\u001b[1;32m 814\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m apply_constraint:\n\u001b[1;32m 815\u001b[0m \u001b[38;5;66;03m# We need a special md flag here because for MD we want\u001b[39;00m\n\u001b[1;32m 816\u001b[0m \u001b[38;5;66;03m# to skip real constraints but include special \"constraints\"\u001b[39;00m\n\u001b[1;32m 817\u001b[0m \u001b[38;5;66;03m# Like Hookean.\u001b[39;00m\n\u001b[1;32m 818\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m constraint \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mconstraints:\n",
|
| 586 |
+
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/ase/calculators/abc.py:30\u001b[0m, in \u001b[0;36mget_forces\u001b[0;34m()\u001b[0m\n\u001b[1;32m 29\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mget_forces\u001b[39m(\u001b[38;5;28mself\u001b[39m, atoms\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mNone\u001b[39;00m):\n\u001b[0;32m---> 30\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mget_property(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mforces\u001b[39m\u001b[38;5;124m'\u001b[39m, atoms)\n",
|
| 587 |
+
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/ase/calculators/calculator.py:538\u001b[0m, in \u001b[0;36mget_property\u001b[0;34m()\u001b[0m\n\u001b[1;32m 535\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39muse_cache:\n\u001b[1;32m 536\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39matoms \u001b[38;5;241m=\u001b[39m atoms\u001b[38;5;241m.\u001b[39mcopy()\n\u001b[0;32m--> 538\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mcalculate(atoms, [name], system_changes)\n\u001b[1;32m 540\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m name \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mresults:\n\u001b[1;32m 541\u001b[0m \u001b[38;5;66;03m# For some reason the calculator was not able to do what we want,\u001b[39;00m\n\u001b[1;32m 542\u001b[0m \u001b[38;5;66;03m# and that is OK.\u001b[39;00m\n\u001b[1;32m 543\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m PropertyNotImplementedError(\n\u001b[1;32m 544\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m not present in this \u001b[39m\u001b[38;5;124m'\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mcalculation\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;241m.\u001b[39mformat(name)\n\u001b[1;32m 545\u001b[0m )\n",
|
| 588 |
+
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/mlip-arena/mlip_arena/models/externals/chgnet.py:36\u001b[0m, in \u001b[0;36mcalculate\u001b[0;34m()\u001b[0m\n\u001b[1;32m 30\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mcalculate\u001b[39m(\n\u001b[1;32m 31\u001b[0m \u001b[38;5;28mself\u001b[39m,\n\u001b[1;32m 32\u001b[0m atoms: Atoms \u001b[38;5;241m|\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m,\n\u001b[1;32m 33\u001b[0m properties: \u001b[38;5;28mlist\u001b[39m \u001b[38;5;241m|\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m,\n\u001b[1;32m 34\u001b[0m system_changes: \u001b[38;5;28mlist\u001b[39m \u001b[38;5;241m|\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m,\n\u001b[1;32m 35\u001b[0m ) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[0;32m---> 36\u001b[0m \u001b[38;5;28msuper\u001b[39m()\u001b[38;5;241m.\u001b[39mcalculate(atoms, properties, system_changes)\n\u001b[1;32m 38\u001b[0m \u001b[38;5;66;03m# for ase.io.write compatibility\u001b[39;00m\n\u001b[1;32m 39\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mresults\u001b[38;5;241m.\u001b[39mpop(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mcrystal_fea\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;28;01mNone\u001b[39;00m)\n",
|
| 589 |
+
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/chgnet/model/dynamics.py:143\u001b[0m, in \u001b[0;36mcalculate\u001b[0;34m()\u001b[0m\n\u001b[1;32m 141\u001b[0m structure \u001b[38;5;241m=\u001b[39m AseAtomsAdaptor\u001b[38;5;241m.\u001b[39mget_structure(atoms)\n\u001b[1;32m 142\u001b[0m graph \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mmodel\u001b[38;5;241m.\u001b[39mgraph_converter(structure)\n\u001b[0;32m--> 143\u001b[0m model_prediction \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mmodel\u001b[38;5;241m.\u001b[39mpredict_graph(\n\u001b[1;32m 144\u001b[0m graph\u001b[38;5;241m.\u001b[39mto(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdevice), task\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mefsm\u001b[39m\u001b[38;5;124m\"\u001b[39m, return_crystal_feas\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m\n\u001b[1;32m 145\u001b[0m )\n\u001b[1;32m 147\u001b[0m \u001b[38;5;66;03m# Convert Result\u001b[39;00m\n\u001b[1;32m 148\u001b[0m factor \u001b[38;5;241m=\u001b[39m \u001b[38;5;241m1\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mmodel\u001b[38;5;241m.\u001b[39mis_intensive \u001b[38;5;28;01melse\u001b[39;00m structure\u001b[38;5;241m.\u001b[39mcomposition\u001b[38;5;241m.\u001b[39mnum_atoms\n",
|
| 590 |
+
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/chgnet/model/model.py:627\u001b[0m, in \u001b[0;36mpredict_graph\u001b[0;34m()\u001b[0m\n\u001b[1;32m 625\u001b[0m n_steps \u001b[38;5;241m=\u001b[39m math\u001b[38;5;241m.\u001b[39mceil(\u001b[38;5;28mlen\u001b[39m(graphs) \u001b[38;5;241m/\u001b[39m batch_size)\n\u001b[1;32m 626\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m step \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mrange\u001b[39m(n_steps):\n\u001b[0;32m--> 627\u001b[0m prediction \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mforward(\n\u001b[1;32m 628\u001b[0m [\n\u001b[1;32m 629\u001b[0m g\u001b[38;5;241m.\u001b[39mto(model_device)\n\u001b[1;32m 630\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m g \u001b[38;5;129;01min\u001b[39;00m graphs[batch_size \u001b[38;5;241m*\u001b[39m step : batch_size \u001b[38;5;241m*\u001b[39m (step \u001b[38;5;241m+\u001b[39m \u001b[38;5;241m1\u001b[39m)]\n\u001b[1;32m 631\u001b[0m ],\n\u001b[1;32m 632\u001b[0m task\u001b[38;5;241m=\u001b[39mtask,\n\u001b[1;32m 633\u001b[0m return_site_energies\u001b[38;5;241m=\u001b[39mreturn_site_energies,\n\u001b[1;32m 634\u001b[0m return_atom_feas\u001b[38;5;241m=\u001b[39mreturn_atom_feas,\n\u001b[1;32m 635\u001b[0m return_crystal_feas\u001b[38;5;241m=\u001b[39mreturn_crystal_feas,\n\u001b[1;32m 636\u001b[0m )\n\u001b[1;32m 637\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m key \u001b[38;5;129;01min\u001b[39;00m {\n\u001b[1;32m 638\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124me\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[1;32m 639\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 644\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mcrystal_fea\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[1;32m 645\u001b[0m } \u001b[38;5;241m&\u001b[39m {\u001b[38;5;241m*\u001b[39mprediction}:\n\u001b[1;32m 646\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m idx, tensor \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28menumerate\u001b[39m(prediction[key]):\n",
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| 591 |
+
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/chgnet/model/model.py:359\u001b[0m, in \u001b[0;36mforward\u001b[0;34m()\u001b[0m\n\u001b[1;32m 354\u001b[0m comp_energy \u001b[38;5;241m=\u001b[39m (\n\u001b[1;32m 355\u001b[0m \u001b[38;5;241m0\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mcomposition_model \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m \u001b[38;5;28;01melse\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mcomposition_model(graphs)\n\u001b[1;32m 356\u001b[0m )\n\u001b[1;32m 358\u001b[0m \u001b[38;5;66;03m# Make batched graph\u001b[39;00m\n\u001b[0;32m--> 359\u001b[0m batched_graph \u001b[38;5;241m=\u001b[39m BatchedGraph\u001b[38;5;241m.\u001b[39mfrom_graphs(\n\u001b[1;32m 360\u001b[0m graphs,\n\u001b[1;32m 361\u001b[0m bond_basis_expansion\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mbond_basis_expansion,\n\u001b[1;32m 362\u001b[0m angle_basis_expansion\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mangle_basis_expansion,\n\u001b[1;32m 363\u001b[0m compute_stress\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124ms\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;129;01min\u001b[39;00m task,\n\u001b[1;32m 364\u001b[0m )\n\u001b[1;32m 366\u001b[0m \u001b[38;5;66;03m# Pass to model\u001b[39;00m\n\u001b[1;32m 367\u001b[0m prediction \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_compute(\n\u001b[1;32m 368\u001b[0m batched_graph,\n\u001b[1;32m 369\u001b[0m compute_force\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;129;01min\u001b[39;00m task,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 374\u001b[0m return_crystal_feas\u001b[38;5;241m=\u001b[39mreturn_crystal_feas,\n\u001b[1;32m 375\u001b[0m )\n",
|
| 592 |
+
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/chgnet/model/model.py:822\u001b[0m, in \u001b[0;36mfrom_graphs\u001b[0;34m()\u001b[0m\n\u001b[1;32m 819\u001b[0m \u001b[38;5;66;03m# Bonds\u001b[39;00m\n\u001b[1;32m 820\u001b[0m atom_cart_coords \u001b[38;5;241m=\u001b[39m graph\u001b[38;5;241m.\u001b[39matom_frac_coord \u001b[38;5;241m@\u001b[39m lattice\n\u001b[1;32m 821\u001b[0m bond_basis_ag, bond_basis_bg, bond_vectors \u001b[38;5;241m=\u001b[39m bond_basis_expansion(\n\u001b[0;32m--> 822\u001b[0m center\u001b[38;5;241m=\u001b[39matom_cart_coords[graph\u001b[38;5;241m.\u001b[39matom_graph[:, \u001b[38;5;241m0\u001b[39m]],\n\u001b[1;32m 823\u001b[0m neighbor\u001b[38;5;241m=\u001b[39matom_cart_coords[graph\u001b[38;5;241m.\u001b[39matom_graph[:, \u001b[38;5;241m1\u001b[39m]],\n\u001b[1;32m 824\u001b[0m undirected2directed\u001b[38;5;241m=\u001b[39mgraph\u001b[38;5;241m.\u001b[39mundirected2directed,\n\u001b[1;32m 825\u001b[0m image\u001b[38;5;241m=\u001b[39mgraph\u001b[38;5;241m.\u001b[39mneighbor_image,\n\u001b[1;32m 826\u001b[0m lattice\u001b[38;5;241m=\u001b[39mlattice,\n\u001b[1;32m 827\u001b[0m )\n\u001b[1;32m 828\u001b[0m atom_positions\u001b[38;5;241m.\u001b[39mappend(atom_cart_coords)\n\u001b[1;32m 829\u001b[0m bond_bases_ag\u001b[38;5;241m.\u001b[39mappend(bond_basis_ag)\n",
|
| 593 |
+
"\u001b[0;31mIndexError\u001b[0m: too many indices for tensor of dimension 1"
|
| 594 |
]
|
| 595 |
}
|
| 596 |
],
|
|
|
|
| 624 |
"name": "python",
|
| 625 |
"nbconvert_exporter": "python",
|
| 626 |
"pygments_lexer": "ipython3",
|
| 627 |
+
"version": "3.11.10"
|
| 628 |
},
|
| 629 |
"widgets": {
|
| 630 |
"application/vnd.jupyter.widget-state+json": {
|
mlip_arena/tasks/diatomics/gpaw/run.ipynb
CHANGED
|
@@ -38,7 +38,7 @@
|
|
| 38 |
{
|
| 39 |
"data": {
|
| 40 |
"application/vnd.jupyter.widget-view+json": {
|
| 41 |
-
"model_id": "
|
| 42 |
"version_major": 2,
|
| 43 |
"version_minor": 0
|
| 44 |
},
|
|
@@ -59,7 +59,7 @@
|
|
| 59 |
{
|
| 60 |
"data": {
|
| 61 |
"application/vnd.jupyter.widget-view+json": {
|
| 62 |
-
"model_id": "
|
| 63 |
"version_major": 2,
|
| 64 |
"version_minor": 0
|
| 65 |
},
|
|
@@ -80,7 +80,7 @@
|
|
| 80 |
{
|
| 81 |
"data": {
|
| 82 |
"application/vnd.jupyter.widget-view+json": {
|
| 83 |
-
"model_id": "
|
| 84 |
"version_major": 2,
|
| 85 |
"version_minor": 0
|
| 86 |
},
|
|
@@ -95,13 +95,13 @@
|
|
| 95 |
"name": "stdout",
|
| 96 |
"output_type": "stream",
|
| 97 |
"text": [
|
| 98 |
-
"Atoms(symbols='N2', pbc=True, cell=[15.0, 15.001, 15.002]
|
| 99 |
]
|
| 100 |
},
|
| 101 |
{
|
| 102 |
"data": {
|
| 103 |
"application/vnd.jupyter.widget-view+json": {
|
| 104 |
-
"model_id": "
|
| 105 |
"version_major": 2,
|
| 106 |
"version_minor": 0
|
| 107 |
},
|
|
@@ -116,13 +116,13 @@
|
|
| 116 |
"name": "stdout",
|
| 117 |
"output_type": "stream",
|
| 118 |
"text": [
|
| 119 |
-
"Atoms(symbols='O2', pbc=True, cell=[15.0, 15.001, 15.002]
|
| 120 |
]
|
| 121 |
},
|
| 122 |
{
|
| 123 |
"data": {
|
| 124 |
"application/vnd.jupyter.widget-view+json": {
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-
"model_id": "
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"version_major": 2,
|
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"version_minor": 0
|
| 128 |
},
|
|
@@ -143,7 +143,7 @@
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|
| 143 |
{
|
| 144 |
"data": {
|
| 145 |
"application/vnd.jupyter.widget-view+json": {
|
| 146 |
-
"model_id": "
|
| 147 |
"version_major": 2,
|
| 148 |
"version_minor": 0
|
| 149 |
},
|
|
@@ -164,7 +164,7 @@
|
|
| 164 |
{
|
| 165 |
"data": {
|
| 166 |
"application/vnd.jupyter.widget-view+json": {
|
| 167 |
-
"model_id": "
|
| 168 |
"version_major": 2,
|
| 169 |
"version_minor": 0
|
| 170 |
},
|
|
@@ -185,7 +185,7 @@
|
|
| 185 |
{
|
| 186 |
"data": {
|
| 187 |
"application/vnd.jupyter.widget-view+json": {
|
| 188 |
-
"model_id": "
|
| 189 |
"version_major": 2,
|
| 190 |
"version_minor": 0
|
| 191 |
},
|
|
@@ -200,13 +200,13 @@
|
|
| 200 |
"name": "stdout",
|
| 201 |
"output_type": "stream",
|
| 202 |
"text": [
|
| 203 |
-
"Atoms(symbols='Na2', pbc=True, cell=[15.5, 15.501, 15.502]
|
| 204 |
]
|
| 205 |
},
|
| 206 |
{
|
| 207 |
"data": {
|
| 208 |
"application/vnd.jupyter.widget-view+json": {
|
| 209 |
-
"model_id": "
|
| 210 |
"version_major": 2,
|
| 211 |
"version_minor": 0
|
| 212 |
},
|
|
@@ -221,13 +221,14 @@
|
|
| 221 |
"name": "stdout",
|
| 222 |
"output_type": "stream",
|
| 223 |
"text": [
|
|
|
|
| 224 |
"Atoms(symbols='Cr2', pbc=True, cell=[15.190000000000001, 15.191, 15.192000000000002], initial_magmoms=..., calculator=SinglePointCalculator(...))\n"
|
| 225 |
]
|
| 226 |
},
|
| 227 |
{
|
| 228 |
"data": {
|
| 229 |
"application/vnd.jupyter.widget-view+json": {
|
| 230 |
-
"model_id": "
|
| 231 |
"version_major": 2,
|
| 232 |
"version_minor": 0
|
| 233 |
},
|
|
@@ -321,7 +322,7 @@
|
|
| 321 |
" restart_fpath = out_dir / 'restart.gpw'\n",
|
| 322 |
"\n",
|
| 323 |
" calc = GPAW(\n",
|
| 324 |
-
" mode=PW(
|
| 325 |
" xc='PBE',\n",
|
| 326 |
" spinpol=True,\n",
|
| 327 |
" # basis='dzp'\n",
|
|
@@ -330,12 +331,8 @@
|
|
| 330 |
" # nbands=0 if element.is_noble_gas else '110%',\n",
|
| 331 |
" hund=False,\n",
|
| 332 |
" mixer=MixerDif(0.01, 1, 1) if element.is_transition_metal else MixerDif(0.25, 3, 10),\n",
|
| 333 |
-
<<<<<<< Updated upstream
|
| 334 |
-
" eigensolver='rmm-diis', #Davidson(3), # This solver can parallelize over bands Davidson(3), #\n",
|
| 335 |
-
=======
|
| 336 |
" # eigensolver='rmm-diis', #Davidson(3), # This solver can parallelize over bands Davidson(3), #\n",
|
| 337 |
-
|
| 338 |
-
" occupations=FermiDirac(0.03, fixmagmom=False), # if not element.is_metal else FermiDirac(0.2, fixmagmom=False),\n",
|
| 339 |
" # eigensolver=LCAOETDM(),\n",
|
| 340 |
" # # searchdir_algo={'name': 'l-bfgs-p', 'memory': 10}),\n",
|
| 341 |
" # occupations={'name': 'fixed-uniform'},\n",
|
|
@@ -349,17 +346,12 @@
|
|
| 349 |
" 'energy': 5e-4,\n",
|
| 350 |
" # 'bands': 4\n",
|
| 351 |
" },\n",
|
| 352 |
-
" parallel={'gpu': True}\n",
|
| 353 |
" # {'energy': 0.0005, # eV / electron\n",
|
| 354 |
" # 'density': 1.0e-4, # electrons / electron\n",
|
| 355 |
" # 'eigenstates': 4.0e-8, # eV^2 / electron\n",
|
| 356 |
" # 'bands': 'occupied'},\n",
|
| 357 |
-
<<<<<<< Updated upstream
|
| 358 |
-
" \n",
|
| 359 |
-
=======
|
| 360 |
" # parallel={'gpu': True},\n",
|
| 361 |
" setups='paw' \n",
|
| 362 |
-
>>>>>>> Stashed changes
|
| 363 |
" )\n",
|
| 364 |
" # calc = GPAW(\n",
|
| 365 |
" # mode='pw', #PW(1500),\n",
|
|
@@ -424,17 +416,17 @@
|
|
| 424 |
"\n",
|
| 425 |
" if fm_energy <= afm_energy:\n",
|
| 426 |
" magmoms = fm_magmoms\n",
|
| 427 |
-
"
|
| 428 |
" # shutil.move(out_dir / \"WAVECAR_FM\", out_dir / \"WAVECAR\") \n",
|
| 429 |
" else:\n",
|
| 430 |
" magmoms = afm_magmoms\n",
|
| 431 |
-
"
|
| 432 |
" # shutil.move(out_dir / \"WAVECAR_AFM\", out_dir / \"WAVECAR\")\n",
|
| 433 |
"\n",
|
| 434 |
-
"
|
| 435 |
-
"
|
| 436 |
"\n",
|
| 437 |
-
"
|
| 438 |
" # m = min(abs(magmoms[0])*1.2, m)\n",
|
| 439 |
" # magmoms = magmoms*m/np.abs(magmoms)\n",
|
| 440 |
"\n",
|
|
@@ -451,20 +443,12 @@
|
|
| 451 |
},
|
| 452 |
{
|
| 453 |
"cell_type": "code",
|
| 454 |
-
"execution_count":
|
| 455 |
"id": "06118461-8db9-49f0-8aae-2150146ab9b5",
|
| 456 |
"metadata": {
|
| 457 |
"tags": []
|
| 458 |
},
|
| 459 |
-
"outputs": [
|
| 460 |
-
{
|
| 461 |
-
"name": "stdout",
|
| 462 |
-
"output_type": "stream",
|
| 463 |
-
"text": [
|
| 464 |
-
"\n"
|
| 465 |
-
]
|
| 466 |
-
}
|
| 467 |
-
],
|
| 468 |
"source": [
|
| 469 |
"!echo $GPAW_NEW"
|
| 470 |
]
|
|
@@ -558,163 +542,104 @@
|
|
| 558 |
"widgets": {
|
| 559 |
"application/vnd.jupyter.widget-state+json": {
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| 560 |
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| 562 |
"model_module": "@jupyter-widgets/controls",
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| 563 |
"model_module_version": "2.0.0",
|
| 564 |
-
"model_name": "
|
| 565 |
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|
| 566 |
-
"
|
| 567 |
-
"
|
| 568 |
-
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|
| 569 |
-
"style": "IPY_MODEL_e09a0c50b3bb4e2ebaba70054dcbbedb",
|
| 570 |
-
"value": 22
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| 571 |
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| 572 |
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| 573 |
-
"
|
| 574 |
"model_module": "@jupyter-widgets/controls",
|
| 575 |
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|
| 576 |
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| 577 |
"state": {
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| 578 |
-
"
|
| 579 |
-
"layout": "IPY_MODEL_74c767383218458094552abeda7cf5a8",
|
| 580 |
-
"max": 16,
|
| 581 |
-
"style": "IPY_MODEL_b9c8d4aba50241e4873535d5253bc431",
|
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-
"value": 8
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| 583 |
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| 584 |
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| 585 |
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"
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| 586 |
-
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| 588 |
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| 589 |
-
"state": {}
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| 590 |
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| 591 |
-
"03f87ed3d767468fa018b33a57eb94cc": {
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| 595 |
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| 596 |
-
"
|
| 597 |
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|
| 598 |
-
|
| 599 |
-
"IPY_MODEL_06455df8a89646fa993fee1979052f1e"
|
| 600 |
-
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|
| 601 |
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"layout": "IPY_MODEL_73bc039f53694da9ab33d38f3105ff84"
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| 609 |
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|
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-
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| 614 |
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"layout": "
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-
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"bar_style": "success",
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"max": 16,
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| 626 |
-
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-
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-
"value": " 0/29 [00:00<?, ?it/s]"
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|
| 667 |
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"text": [
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+
"Did not converge! See text output for help.\n",
|
| 225 |
"Atoms(symbols='Cr2', pbc=True, cell=[15.190000000000001, 15.191, 15.192000000000002], initial_magmoms=..., calculator=SinglePointCalculator(...))\n"
|
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]
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{
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},
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" restart_fpath = out_dir / 'restart.gpw'\n",
|
| 323 |
"\n",
|
| 324 |
" calc = GPAW(\n",
|
| 325 |
+
" mode=PW(2000),\n",
|
| 326 |
" xc='PBE',\n",
|
| 327 |
" spinpol=True,\n",
|
| 328 |
" # basis='dzp'\n",
|
|
|
|
| 331 |
" # nbands=0 if element.is_noble_gas else '110%',\n",
|
| 332 |
" hund=False,\n",
|
| 333 |
" mixer=MixerDif(0.01, 1, 1) if element.is_transition_metal else MixerDif(0.25, 3, 10),\n",
|
|
|
|
|
|
|
|
|
|
| 334 |
" # eigensolver='rmm-diis', #Davidson(3), # This solver can parallelize over bands Davidson(3), #\n",
|
| 335 |
+
" occupations=FermiDirac(0.2, fixmagmom=False), # if not element.is_metal else FermiDirac(0.2, fixmagmom=False),\n",
|
|
|
|
| 336 |
" # eigensolver=LCAOETDM(),\n",
|
| 337 |
" # # searchdir_algo={'name': 'l-bfgs-p', 'memory': 10}),\n",
|
| 338 |
" # occupations={'name': 'fixed-uniform'},\n",
|
|
|
|
| 346 |
" 'energy': 5e-4,\n",
|
| 347 |
" # 'bands': 4\n",
|
| 348 |
" },\n",
|
|
|
|
| 349 |
" # {'energy': 0.0005, # eV / electron\n",
|
| 350 |
" # 'density': 1.0e-4, # electrons / electron\n",
|
| 351 |
" # 'eigenstates': 4.0e-8, # eV^2 / electron\n",
|
| 352 |
" # 'bands': 'occupied'},\n",
|
|
|
|
|
|
|
|
|
|
| 353 |
" # parallel={'gpu': True},\n",
|
| 354 |
" setups='paw' \n",
|
|
|
|
| 355 |
" )\n",
|
| 356 |
" # calc = GPAW(\n",
|
| 357 |
" # mode='pw', #PW(1500),\n",
|
|
|
|
| 416 |
"\n",
|
| 417 |
" if fm_energy <= afm_energy:\n",
|
| 418 |
" magmoms = fm_magmoms\n",
|
| 419 |
+
" atoms.set_initial_magnetic_moments(magmoms) \n",
|
| 420 |
" # shutil.move(out_dir / \"WAVECAR_FM\", out_dir / \"WAVECAR\") \n",
|
| 421 |
" else:\n",
|
| 422 |
" magmoms = afm_magmoms\n",
|
| 423 |
+
" atoms.set_initial_magnetic_moments(magmoms)\n",
|
| 424 |
" # shutil.move(out_dir / \"WAVECAR_AFM\", out_dir / \"WAVECAR\")\n",
|
| 425 |
"\n",
|
| 426 |
+
"# if i > 0: \n",
|
| 427 |
+
"# magmoms = atoms.get_magnetic_moments()\n",
|
| 428 |
"\n",
|
| 429 |
+
"# atoms.set_initial_magnetic_moments(magmoms)\n",
|
| 430 |
" # m = min(abs(magmoms[0])*1.2, m)\n",
|
| 431 |
" # magmoms = magmoms*m/np.abs(magmoms)\n",
|
| 432 |
"\n",
|
|
|
|
| 443 |
},
|
| 444 |
{
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| 445 |
"cell_type": "code",
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| 446 |
+
"execution_count": null,
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"id": "06118461-8db9-49f0-8aae-2150146ab9b5",
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| 448 |
"metadata": {
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| 450 |
},
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+
"outputs": [],
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|
|
|
|
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| 452 |
"source": [
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| 453 |
"!echo $GPAW_NEW"
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]
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|
|
| 819 |
"model_module_version": "2.0.0",
|
| 820 |
"model_name": "LayoutModel",
|
| 821 |
"state": {}
|
| 822 |
},
|
| 823 |
+
"faf0fccdc8044bc69f12c930c57d4e9f": {
|
|
|
|
|
|
|
|
|
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|
| 824 |
"model_module": "@jupyter-widgets/controls",
|
| 825 |
"model_module_version": "2.0.0",
|
| 826 |
"model_name": "HTMLStyleModel",
|
mlip_arena/tasks/diatomics/vasp/homonuclear-diatomics.json
CHANGED
|
@@ -1,3 +1,3 @@
|
|
| 1 |
version https://git-lfs.github.com/spec/v1
|
| 2 |
-
oid sha256:
|
| 3 |
-
size
|
|
|
|
| 1 |
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:56b866aaf640e4a2ac46d74fe01ced6ceb25c69329569344172884302c004b7e
|
| 3 |
+
size 14107
|
mlip_arena/tasks/eos/run.ipynb
CHANGED
|
@@ -2,7 +2,7 @@
|
|
| 2 |
"cells": [
|
| 3 |
{
|
| 4 |
"cell_type": "code",
|
| 5 |
-
"execution_count":
|
| 6 |
"metadata": {},
|
| 7 |
"outputs": [
|
| 8 |
{
|
|
@@ -11,11 +11,21 @@
|
|
| 11 |
"text": [
|
| 12 |
"No module named 'deepmd'\n"
|
| 13 |
]
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 14 |
}
|
| 15 |
],
|
| 16 |
"source": [
|
| 17 |
"import os\n",
|
| 18 |
-
"from mp_api.client import MPRester\n",
|
| 19 |
"from dask.distributed import Client\n",
|
| 20 |
"from dask_jobqueue import SLURMCluster\n",
|
| 21 |
"from prefect import task, flow\n",
|
|
@@ -34,7 +44,7 @@
|
|
| 34 |
"\n",
|
| 35 |
"load_dotenv()\n",
|
| 36 |
"\n",
|
| 37 |
-
"MP_API_KEY = os.environ.get(\"MP_API_KEY\", None)"
|
| 38 |
]
|
| 39 |
},
|
| 40 |
{
|
|
@@ -575,7 +585,7 @@
|
|
| 575 |
"name": "python",
|
| 576 |
"nbconvert_exporter": "python",
|
| 577 |
"pygments_lexer": "ipython3",
|
| 578 |
-
"version": "3.11.
|
| 579 |
},
|
| 580 |
"widgets": {
|
| 581 |
"application/vnd.jupyter.widget-state+json": {
|
|
|
|
| 2 |
"cells": [
|
| 3 |
{
|
| 4 |
"cell_type": "code",
|
| 5 |
+
"execution_count": 2,
|
| 6 |
"metadata": {},
|
| 7 |
"outputs": [
|
| 8 |
{
|
|
|
|
| 11 |
"text": [
|
| 12 |
"No module named 'deepmd'\n"
|
| 13 |
]
|
| 14 |
+
},
|
| 15 |
+
{
|
| 16 |
+
"data": {
|
| 17 |
+
"text/plain": [
|
| 18 |
+
"True"
|
| 19 |
+
]
|
| 20 |
+
},
|
| 21 |
+
"execution_count": 2,
|
| 22 |
+
"metadata": {},
|
| 23 |
+
"output_type": "execute_result"
|
| 24 |
}
|
| 25 |
],
|
| 26 |
"source": [
|
| 27 |
"import os\n",
|
| 28 |
+
"# from mp_api.client import MPRester\n",
|
| 29 |
"from dask.distributed import Client\n",
|
| 30 |
"from dask_jobqueue import SLURMCluster\n",
|
| 31 |
"from prefect import task, flow\n",
|
|
|
|
| 44 |
"\n",
|
| 45 |
"load_dotenv()\n",
|
| 46 |
"\n",
|
| 47 |
+
"# MP_API_KEY = os.environ.get(\"MP_API_KEY\", None)"
|
| 48 |
]
|
| 49 |
},
|
| 50 |
{
|
|
|
|
| 585 |
"name": "python",
|
| 586 |
"nbconvert_exporter": "python",
|
| 587 |
"pygments_lexer": "ipython3",
|
| 588 |
+
"version": "3.11.10"
|
| 589 |
},
|
| 590 |
"widgets": {
|
| 591 |
"application/vnd.jupyter.widget-state+json": {
|