Added FilePad demonstration files in demos subfolder

demos/7_filepad/.gitignore

+.ipynb_checkpoints
\ No newline at end of file

demos/7_filepad/A_cluster.yaml

+fw_id: -20
+name: "Minimize cluster"
+spec:
+  _category: "bwcloud_noqueue"
+  _files_out:
+    data_file: final.lammps
+  _tasks:
+  - _fw_name: GetFilesTask
+    identifiers:
+    - fireworks-hands-on-2019-12-09/potential
+    new_file_names:
+    - Au-Grochola-JCP05.eam.alloy
+  - _fw_name: GetFilesTask
+    identifiers:
+    - fireworks-hands-on-2019-12-09/small_cluster
+    new_file_names:
+    - initial.lammps
+  - _fw_name: GetFilesTask
+    identifiers:
+    - fireworks-hands-on-2019-12-09/minimize_cluster
+    new_file_names:
+    - lammps.in
+  - _fw_name: ScriptTask
+    script: source /etc/profile; module load LAMMPS; mpirun -n 2 lmp -in lammps.in

demos/7_filepad/A_substrate.yaml

+fw_id: -10
+name: "Minimize substrate"
+spec:
+  _category: "bwcloud_noqueue"
+  _files_out: 
+     data_file: final.lammps
+  _tasks:
+  - _fw_name: GetFilesTask
+    identifiers:
+    - fireworks-hands-on-2019-12-09/potential
+    new_file_names:
+    - Au-Grochola-JCP05.eam.alloy
+  - _fw_name: GetFilesTask
+    identifiers:
+    - fireworks-hands-on-2019-12-09/minimize_substrate
+    new_file_names:
+    - lammps.in
+  - _fw_name: ScriptTask
+    script: source /etc/profile; module load LAMMPS; mpirun -n 2 lmp -in lammps.in

demos/7_filepad/B_cluster.yaml

+fw_id: -40
+name: "Equilibrate cluster"
+spec:
+  _category: "bwcloud_noqueue"
+  _files_in:
+    data_file: initial.lammps
+  _files_out:
+    data_file: final.lammps
+  _tasks:
+  - _fw_name: GetFilesTask
+    identifiers:
+    - fireworks-hands-on-2019-12-09/potential
+    new_file_names:
+    - Au-Grochola-JCP05.eam.alloy
+  - _fw_name: GetFilesTask
+    identifiers:
+    - fireworks-hands-on-2019-12-09/equilibrate_cluster
+    new_file_names:
+    - lammps.in
+  - _fw_name: ScriptTask
+    script: source /etc/profile; module load LAMMPS; mpirun -n 2 lmp -in lammps.in

demos/7_filepad/B_substrate.yaml

+fw_id: -30
+name: "Equilibrate substrate"
+spec:
+  _category: "bwcloud_noqueue"
+  _files_in:
+    data_file: initial.lammps
+  _files_out:
+    data_file_substrate: final.lammps
+  _tasks:
+  - _fw_name: GetFilesTask
+    identifiers:
+    - fireworks-hands-on-2019-12-09/potential
+    new_file_names:
+    - Au-Grochola-JCP05.eam.alloy
+  - _fw_name: GetFilesTask
+    identifiers:
+    - fireworks-hands-on-2019-12-09/equilibrate_substrate
+    new_file_names:
+    - lammps.in
+  - _fw_name: ScriptTask
+    script: source /etc/profile; module load LAMMPS; mpirun -n 2 lmp -in lammps.in

demos/7_filepad/C_cluster.yaml

+fw_id: -50 
+name: "Melt cluster"
+spec:
+  _category: "bwcloud_noqueue"
+  _files_in:
+    data_file: initial.lammps
+  _files_out:
+    data_file_cluster: final.lammps
+  _tasks:
+  - _fw_name: GetFilesTask
+    identifiers:
+    - fireworks-hands-on-2019-12-09/potential
+    new_file_names:
+    - Au-Grochola-JCP05.eam.alloy
+  - _fw_name: GetFilesTask
+    identifiers:
+    - fireworks-hands-on-2019-12-09/equilibrate_cluster
+    new_file_names:
+    - lammps.in
+  - _fw_name: ScriptTask
+    script: source /etc/profile; module load LAMMPS; mpirun -n 2 lmp -in lammps.in

demos/7_filepad/D_deposit.yaml

+fw_id: -60
+name: "Deposit"
+spec:
+  _category: "bwcloud_noqueue"
+  _files_in:
+    data_file_cluster: cluster.lammps
+    data_file_substrate: substrate.lammps
+  _tasks:
+  - _fw_name: GetFilesTask
+    identifiers:
+    - fireworks-hands-on-2019-12-09/potential
+    new_file_names:
+    - Au-Grochola-JCP05.eam.alloy
+  - _fw_name: GetFilesTask
+    identifiers:
+    - fireworks-hands-on-2019-12-09/deposit
+    new_file_names:
+    - lammps.in
+  - _fw_name: ScriptTask
+    script: source /etc/profile; module load LAMMPS; mpirun -n 2 lmp -in lammps.in
+  - _fw_name: AddFilesTask
+    paths: 
+    - traj.dump
+    compress: True
+    metadata: 
+      project:  fireworks-hands-on-2019-12-09
+      type:     trajectory
+      velocity: -25
+      steps:    4000
+      timestep: 0.001
+  - _fw_name: AddFilesTask
+    paths: 
+    - final.lammps
+    compress: True
+    metadata: 
+      project:  fireworks-hands-on-2019-12-09
+      type:     final configuration
+      velocity: -25
+      steps:    4000
+      timestep: 0.001
+  - _fw_name: AddFilesTask
+    paths: 
+    - log.lammps
+    compress: True
+    metadata: 
+      project:  fireworks-hands-on-2019-12-09
+      type:     log
+      velocity: -25
+      steps:    4000
+      timestep: 0.001

demos/7_filepad/README.md

+# FireWorks, FilePad and metadata
+
+## Introduction
+
+The Jupyter notebook `PythonGoldCluster.ipynb` contains two
+[FireWorks](https://materialsproject.github.io/fireworks/) sample usage
+cases. They demonstrate meaningful use of metadata for management of workflow
+results within FireWork's *FilePad*.
+
+## Content
+
+* `PythonGoldCluster.ipynb`: a Jupyter notebook working through this demo
+  from setting up workflows to anaylizing results, i.e.  from beginning to end
+* `A_*.yaml` to `D_*.yaml`: Static yaml descriptions of FireWorks used within
+  the first sample case.
+* `infiles/*`: static LAMMPS input scripts and data files used in both sample
+  cases. The third-party EAM potential file `Au-Grochola-JCP05.eam.alloy` by
+
+    *G. Grochola, S.P. Russo, and I.K. Snook (2005), "On fitting a gold embedded
+    atom method potential using the force matching method", The Journal of
+    Chemical Physics, 123(20), 204719. DOI: 10.1063/1.2124667.*
+
+  has been excluded from this repository. You will find it publically available
+  for download at https://www.ctcms.nist.gov/potentials/system/Au
+  (see `infiles/NOTE`)
+* `fig/*`: figures and animations used for documentation purposes
+* `doc/PythonGoldCluster.html`: a static HTML-rendered version of the Jupyter
+  notebook. Does not include any interactive trajectory visualizations via
+  `nglview`.
+* `doc/FilePad_slides.pdf`: static PDF-rendered slides outlining this
+  demonstration's core concepts.
+* `doc/gold_droplet_impact.mp4`: An accompanying gold droplet impact animation
+  not embedded within the static PDF slides.
+
+## Requirements
+
+The Jupyter notebook has been tested with FireWorks version 1.9.5.
+Next to FireWorks, the Python packages
+* ase
+* matplotlib
+* nglview (indirectly via ASE)
+* numpy
+* pandas
+* scipy
+are used to facilitate demonstrative analysis of results.
+
+The samples have been designed to run on a custom OpenStack instance. An image
+of this instance is available on request from the author (Johannes Hörmann,
+johannes.hoermann@imtek.uni-freiburg.de) via the OpenSzack service *bwCloud*
+(https://bwcloud.ruf.uni-freiburg.de). Without modifications, these samples will
+not run within the framework of this *grk2450-fireworks-tutorial*. Most
+importantly, every FirwWork's "_category" spec must point to a worker that
+offers a LAMMPS executable. Likewise, *ScriptTask* calls of LAMMPS must
+match this particular worker's setup.
+
+The LAMMPS versio used for this demonstration is
+
+    LAMMPS (22 Aug 2018)
+
+and the executable has been built with
+
+    Active compile time flags:
+
+    -DLAMMPS_GZIP
+    -DLAMMPS_PNG
+    -DLAMMPS_JPEG
+    -DLAMMPS_FFMPEG
+
+    Installed packages:
+
+    COLLOID COMPRESS KOKKOS KSPACE MANYBODY MC MOLECULE MPIIO OPT PYTHON REPLICA
+    RIGID VORONOI USER-COLVARS USER-DIFFRACTION USER-MOLFILE USER-NETCDF USER-OMP
+
+
+## Contributors:
+
+* Johannes Hörmann (IMTEK, University of Freiburg, johannes.hoermann@imtek.uni-freiburg.de)
+* Prof. Lars Pastewka (IMTEK, University of Freiburg, lars.pastewka@imtek.uni-freiburg.de)

demos/7_filepad/infiles/A_minimize_cluster.in

+# LAMMPS input files contain a list of commands that are executed in order of
+# appearance. General structure is
+#   <command>  <parameters>
+# All possible commands are listed at:
+#   http://lammps.sandia.gov/doc/Section_commands.html
+# LAMMPS will ignore lines that start with a '#'
+
+dimension      3
+# The next statement is new. Default is "units lj". This sets units to
+#   Angstroms (distance), ps (time), g/mol (mass), Kelvin (temperature), ...
+units          metal
+# Nonperiodic - we want a cluster (in vacuum)
+boundary       s s s
+atom_style     atomic
+
+#read_data      cluster_923.lammps
+read_data      initial.lammps
+
+# This defines an embedded-atom method potential. Au_u3.eam is the parameter
+# file. Open it in an editor.
+pair_style     eam/alloy
+pair_coeff     * * Au-Grochola-JCP05.eam.alloy Au
+
+thermo         100
+thermo_style   custom step ke pe etotal temp press
+thermo_modify  norm no
+
+dump           1 all custom 100 traj.dump id type x y z vx vy vz
+
+minimize       0.0 1e-3 1000000 1000000
+
+write_data     final.lammps

demos/7_filepad/infiles/A_minimize_substrate.in

+# LAMMPS input files contain a list of commands that are executed in order of
+# appearance. General structure is
+#   <command>  <parameters>
+# All possible commands are listed at:
+#   http://lammps.sandia.gov/doc/Section_commands.html
+# LAMMPS will ignore lines that start with a '#'
+
+dimension      3
+units          metal
+boundary       p p s
+atom_style     atomic
+
+lattice        fcc 4.08
+region         substrate block -6 14  -6 14  -20 -15
+create_box     1 substrate
+create_atoms   1 region substrate
+group          substrate region substrate
+
+pair_style     eam/alloy
+pair_coeff     * * Au-Grochola-JCP05.eam.alloy Au
+
+thermo         100
+thermo_style   custom step ke pe etotal temp press
+thermo_modify  norm no
+
+dump           1 all custom 100 traj.dump id type x y z vx vy vz
+
+minimize       0.0 1e-3 1000000 1000000
+
+write_data     final.lammps

demos/7_filepad/infiles/B_equilibrate_cluster.in

+# LAMMPS input files contain a list of commands that are executed in order of
+# appearance. General structure is
+#   <command>  <parameters>
+# All possible commands are listed at:
+#   http://lammps.sandia.gov/doc/Section_commands.html
+# LAMMPS will ignore lines that start with a '#'
+
+dimension      3
+# The next statement is new. Default is "units lj". This sets units to
+#   Angstroms (distance), ps (time), g/mol (mass), Kelvin (temperature), ...
+units          metal
+# Nonperiodic, we want a cluster (in vacuum)
+boundary       s s s
+atom_style     atomic
+
+read_data      initial.lammps
+
+# Set an initial temperature. Temperature are in Kelvins now!
+velocity       all create 100 1229832
+
+pair_style     eam/alloy
+pair_coeff     * * Au-Grochola-JCP05.eam.alloy Au
+
+thermo         10
+thermo_style   custom step ke pe etotal temp press
+thermo_modify  norm no
+
+dump           1 all custom 1 traj.dump id type x y z vx vy vz
+
+fix            1 all nve
+
+# Timestep is in ps! Time steps are on the order of 1 fs.
+timestep       0.005
+run            1000
+
+write_data     final.lammps
\ No newline at end of file

demos/7_filepad/infiles/B_equilibrate_substrate.in

+# LAMMPS input files contain a list of commands that are executed in order of
+# appearance. General structure is
+#   <command>  <parameters>
+# All possible commands are listed at:
+#   http://lammps.sandia.gov/doc/Section_commands.html
+# LAMMPS will ignore lines that start with a '#'
+
+dimension      3
+# The next statement is new. Default is "units lj". This sets units to
+#   Angstroms (distance), ps (time), g/mol (mass), Kelvin (temperature), ...
+units          metal
+# Nonperiodic, we want a cluster (in vacuum)
+boundary       p p s
+atom_style     atomic
+
+read_data      initial.lammps
+
+# Set an initial temperature. Temperature are in Kelvins now!
+velocity       all create 100 1229832
+
+pair_style     eam/alloy
+pair_coeff     * * Au-Grochola-JCP05.eam.alloy Au
+
+thermo         1000
+thermo_style   custom step ke pe etotal temp press
+thermo_modify  norm no
+
+dump           1 all custom 100 traj.dump id type x y z vx vy vz
+
+fix            1 all nve
+
+# Timestep is in ps! Time steps are on the order of 1 fs.
+timestep       0.001
+run            1000
+
+write_data     final.lammps
\ No newline at end of file

demos/7_filepad/infiles/C_melt_cluster.in

+# LAMMPS input files contain a list of commands that are executed in order of
+# appearance. General structure is
+#   <command>  <parameters>
+# All possible commands are listed at:
+#   http://lammps.sandia.gov/doc/Section_commands.html
+# LAMMPS will ignore lines that start with a '#'
+
+dimension      3
+# The next statement is new. Default is "units lj". This sets units to
+#   Angstroms (distance), ps (time), g/mol (mass), Kelvin (temperature), ...
+units          metal
+# Nonperiodic, we want a cluster (in vacuum)
+boundary       s s s
+atom_style     atomic
+
+read_data      initial.lammps
+
+# Set an initial temperature. Temperature are in Kelvins now!
+velocity       all create 300 1229832
+
+pair_style     eam/alloy
+pair_coeff     * * Au-Grochola-JCP05.eam.alloy Au
+
+thermo         1000
+thermo_style   custom step ke pe etotal temp press
+thermo_modify  norm no
+
+dump           1 all custom 100 traj.dump id type x y z vx vy vz
+
+fix            1 all nve
+# This rescales the temperature every 1000 time steps.
+fix            2 all temp/rescale 500 100 1800 0.0 1.0
+# This is new. Output a couple of (global) quantities to a separate file, akin
+# to the thermo command above. Quantities are averaged.
+# After rescaling velocities, we wait for 500 steps for relaxation and then
+# average over the remaining 500 steps.
+fix            3 all ave/time 1 500 1000 c_thermo_pe c_thermo_temp c_thermo_press file ave.out
+
+# Timestep is in ps! Time steps are on the order of 1 fs.
+timestep       0.01
+run            10000
+
+write_data     final.lammps

demos/7_filepad/infiles/D_deposit.in

+# LAMMPS input files contain a list of commands that are executed in order of
+# appearance. General structure is
+#   <command>  <parameters>
+# All possible commands are listed at:
+#   http://lammps.sandia.gov/doc/Section_commands.html
+# LAMMPS will ignore lines that start with a '#'
+variable vel   index -25
+variable steps index 4000
+# override on command line, i.e. via "-v vel -30"
+
+dimension      3
+units          metal
+boundary       p p s
+atom_style     atomic
+
+read_data     cluster.lammps
+group         cluster type 1
+read_data     substrate.lammps add append offset 0 0 0 0 0 shift 0 0 0
+
+group          substrate subtract all cluster
+
+velocity       cluster set 0 0 ${vel} sum yes
+
+pair_style     eam/alloy
+pair_coeff     * * Au-Grochola-JCP05.eam.alloy Au
+
+thermo         10
+thermo_style   custom step ke pe etotal temp press
+thermo_modify  norm no
+
+dump           1 all custom 100 traj.dump id type x y z vx vy vz
+
+fix            1 all nve
+
+timestep       0.001
+run            ${steps}
+
+write_data     final.lammps