From 8d993bc1f0dd46515356f06e4bc20304f8227a78 Mon Sep 17 00:00:00 2001
From: Ivan Kondov <ivan.kondov@kit.edu>
Date: Thu, 18 Feb 2021 15:27:54 +0100
Subject: [PATCH] adapted wf input and qadapter to fh2, tm calculation in two
steps
---
.../config/qadapter_fh2_turbomole.yaml | 10 +--
demos/6_advanced/inputs/water-turbomole.yaml | 6 +-
.../inputs/water-turbomole_freqs.yaml | 35 ++++++++++
.../inputs/water-turbomole_relax.yaml | 64 +++++++++++++++++++
4 files changed, 107 insertions(+), 8 deletions(-)
create mode 100644 demos/6_advanced/inputs/water-turbomole_freqs.yaml
create mode 100644 demos/6_advanced/inputs/water-turbomole_relax.yaml
diff --git a/demos/6_advanced/config/qadapter_fh2_turbomole.yaml b/demos/6_advanced/config/qadapter_fh2_turbomole.yaml
index acedd7f..907401d 100644
--- a/demos/6_advanced/config/qadapter_fh2_turbomole.yaml
+++ b/demos/6_advanced/config/qadapter_fh2_turbomole.yaml
@@ -1,11 +1,11 @@
_fw_name: CommonAdapter
_fw_q_type: SLURM
-rocket_launch: rlaunch -w /home/kit/scc/jk7683/grk2450-fireworks-tutorial/advanced/config/fworker_turbomole.yaml -l /home/kit/scc/jk7683/grk2450-fireworks-tutorial/advanced/config/launchpad.yaml rapidfire --nlaunches 1
+rocket_launch: rlaunch -w /home/fh2-project-devel/jk7683/grk2450-fireworks-tutorial/demos/6_advanced/config/fworker_fh2_turbomole.yaml -l /home/fh2-project-devel/jk7683/.fireworks/launchpad_mongonm1_test.yaml rapidfire --nlaunches 1
nodes: 1
-ntasks: 20
-walltime: '00:30:00'
-queue: normal
+ntasks: 2
+walltime: '00:10:00'
+queue: develop
account: null
job_name: null
-pre_rocket: export PARA_ARCH=MPI; module purge; module load anaconda3 chem/turbomole; export PYTHONPATH=/home/kit/scc/jk7683/grk2450-fireworks-tutorial/lib:$PYTHONPATH
+pre_rocket: module use $PROJECT/modulefiles; module purge; export PARA_ARCH=MPI; module load anaconda3 chem/turbomole; export PYTHONPATH=/home/fh2-project-devel/jk7683/grk2450-fireworks-tutorial/lib:$PYTHONPATH
post_rocket: null
diff --git a/demos/6_advanced/inputs/water-turbomole.yaml b/demos/6_advanced/inputs/water-turbomole.yaml
index ace0525..e3d6616 100644
--- a/demos/6_advanced/inputs/water-turbomole.yaml
+++ b/demos/6_advanced/inputs/water-turbomole.yaml
@@ -3,7 +3,7 @@ fws:
name: Relax H2O structure
spec:
_category: turbomole
- _fworker: uc1
+ _fworker: fh2
_dupefinder:
_fw_name: DupeFinderExact
_tasks:
@@ -60,7 +60,7 @@ fws:
name: Normal mode analysis of H2O (numerical derivatives)
spec:
_category: turbomole
- _fworker: uc1
+ _fworker: fh2
_dupefinder:
_fw_name: DupeFinderExact
_tasks:
@@ -106,7 +106,7 @@ fws:
name: Normal mode analysis of H2O (analytical derivatives)
spec:
_category: turbomole
- _fworker: uc1
+ _fworker: fh2
_dupefinder:
_fw_name: DupeFinderExact
_tasks:
diff --git a/demos/6_advanced/inputs/water-turbomole_freqs.yaml b/demos/6_advanced/inputs/water-turbomole_freqs.yaml
new file mode 100644
index 0000000..b6c0424
--- /dev/null
+++ b/demos/6_advanced/inputs/water-turbomole_freqs.yaml
@@ -0,0 +1,35 @@
+fws:
+- fw_id: -3
+ name: Normal mode analysis of H2O (analytical derivatives)
+ spec:
+ _category: turbomole
+ _fworker: fh2
+ _dupefinder:
+ _fw_name: DupeFinderExact
+ _tasks:
+ - _fw_name: PyTask
+ func: compchem.calculate_vibrations
+ inputs:
+ - relaxed structure
+ - constraints
+ - calculator
+ outputs:
+ - vibrational energies
+ - zero-point energy
+ - transition state
+ - energy minimum
+ calculator:
+ name: turbomole
+ parameters:
+ task: frequencies
+ multiplicity: 1
+ total charge: 0
+ basis set name: def-SV(P)
+ use dft: true
+ use resolution of identity: true
+ density functional: pbe
+ density convergence: 1e-8
+ constraints: []
+links:
+ '-3': []
+metadata: {}
diff --git a/demos/6_advanced/inputs/water-turbomole_relax.yaml b/demos/6_advanced/inputs/water-turbomole_relax.yaml
new file mode 100644
index 0000000..1c24716
--- /dev/null
+++ b/demos/6_advanced/inputs/water-turbomole_relax.yaml
@@ -0,0 +1,64 @@
+fws:
+- fw_id: 1
+ name: Relax H2O structure
+ spec:
+ _category: turbomole
+ _fworker: fh2
+ _dupefinder:
+ _fw_name: DupeFinderExact
+ _tasks:
+ - _fw_name: PyTask
+ func: compchem.structure_relaxation
+ inputs:
+ - structure
+ - constraints
+ - calculator
+ outputs:
+ - relaxed structure
+ - energy
+ - forces
+ - dipole
+ calculator:
+ name: turbomole
+ parameters:
+ task: optimize
+ multiplicity: 1
+ total charge: 0
+ use redundant internals: true
+ basis set name: def-SV(P)
+ use dft: true
+ use resolution of identity: true
+ density functional: pbe
+ force convergence: 0.005
+ geometry optimization iterations: 100
+ structure:
+ atoms:
+ cell:
+ - - 12.0
+ - 0.0
+ - 0.0
+ - - 0.0
+ - 12.0
+ - 0.0
+ - - 0.0
+ - 0.0
+ - 12.0
+ numbers: [8, 1, 1]
+ pbc: [true, true, true]
+ positions:
+ - - 6.0
+ - 6.0
+ - 6.0
+ - - 6.96504783
+ - 5.87761163
+ - 6.0
+ - - 5.87761163
+ - 6.96504783
+ - 6.0
+ constraints: []
+links:
+ '1': []
+metadata:
+ density functional: PBE
+ calculator: turbomole
+name: H2O normal modes - extend as you go
--
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