remove lammps-UD

mosdef-hub · Mar 6, 2024 · bd18b67 · bd18b67
1 parent 86fa645
commit bd18b67
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Showing 31 changed files with 12 additions and 1,368 deletions.
diff --git a/reproducibility_project/aggregate_summary/aggregate_init.py b/reproducibility_project/aggregate_summary/aggregate_init.py
@@ -31,9 +31,8 @@ def dict_product(dd):
     "gromacs",
     "hoomd",
     "lammps-VU",
-    #    "lammps-UD",
 ]
-md_engines = ["gromacs", "hoomd", "lammps-VU"]  # , "lammps-UD"]
+md_engines = ["gromacs", "hoomd", "lammps-VU"]
 mc_engines = ["cassandra", "mcccs", "gomc"]
 forcefields = {}
 r_cuts = {}

diff --git a/reproducibility_project/bin/clean_by_engine.sh b/reproducibility_project/bin/clean_by_engine.sh
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 echo Removing jobs from all engines but $1
-for ENGINE in cassandra mcccs gomc gromacs hoomd lammps-VU lammps-UD
+for ENGINE in cassandra mcccs gomc gromacs hoomd lammps-VU
 do
     if [[ $ENGINE != $1 ]]
     then

diff --git a/reproducibility_project/init.py b/reproducibility_project/init.py
@@ -32,9 +32,8 @@ def dict_product(dd):
     "gromacs",
     "hoomd",
     "lammps-VU",
-    # "lammps-UD",
 ]
-md_engines = ["gromacs", "hoomd", "lammps-VU"]  # , "lammps-UD"]
+md_engines = ["gromacs", "hoomd", "lammps-VU"]
 mc_engines = ["cassandra", "mcccs", "gomc"]
 forcefields = {}
 r_cuts = {}

diff --git a/reproducibility_project/lrc_shift_subproject/aggregate_summary/aggregate_init.py b/reproducibility_project/lrc_shift_subproject/aggregate_summary/aggregate_init.py
@@ -16,9 +16,8 @@
     "gromacs",
     "hoomd",
     "lammps-VU",
-    "lammps-UD",
 ]
-md_engines = ["gromacs", "hoomd", "lammps-VU", "lammps-UD"]
+md_engines = ["gromacs", "hoomd", "lammps-VU"]
 mc_engines = ["cassandra", "mcccs", "gomc"]
 forcefields = {}
 r_cuts = {}

diff --git a/reproducibility_project/lrc_shift_subproject/src/engine_input/lammps-UD/.keep b/reproducibility_project/lrc_shift_subproject/src/engine_input/lammps-UD/.keep
diff --git a/reproducibility_project/lrc_shift_subproject/src/engines/lammps-UD/.keep b/reproducibility_project/lrc_shift_subproject/src/engines/lammps-UD/.keep
diff --git a/reproducibility_project/lrc_shift_subproject/subproject-analysis.py b/reproducibility_project/lrc_shift_subproject/subproject-analysis.py
@@ -36,7 +36,7 @@ def add_args(cls, parser):
 
 
 mc_engines = ("gomc", "mcccs", "cassandra")
-md_engines = ("gromacs", "hoomd", "lammps-VU")  # , "lammps-UD")
+md_engines = ("gromacs", "hoomd", "lammps-VU")
 md_npt_props = [
     "potential_energy",
     "kinetic_energy",

diff --git a/reproducibility_project/lrc_shift_subproject/subproject-init.py b/reproducibility_project/lrc_shift_subproject/subproject-init.py
@@ -17,9 +17,8 @@
     "gromacs",
     "hoomd",
     "lammps-VU",
-    "lammps-UD",
 ]
-md_engines = ["gromacs", "hoomd", "lammps-VU", "lammps-UD"]
+md_engines = ["gromacs", "hoomd", "lammps-VU"]
 mc_engines = ["cassandra", "mcccs", "gomc"]
 forcefields = {}
 r_cuts = {}

diff --git a/reproducibility_project/project-analysis.py b/reproducibility_project/project-analysis.py
@@ -36,7 +36,7 @@ def add_args(cls, parser):
 
 
 mc_engines = ("gomc", "mcccs", "cassandra")
-md_engines = ("gromacs", "hoomd", "lammps-VU")  # , "lammps-UD")
+md_engines = ("gromacs", "hoomd", "lammps-VU")
 md_npt_props = [
     "potential_energy",
     "kinetic_energy",

diff --git a/reproducibility_project/spe_subproject/bin/clean_by_engine.sh b/reproducibility_project/spe_subproject/bin/clean_by_engine.sh
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 echo Removing jobs from all engines but $1
-for ENGINE in cassandra mcccs gomc gromacs hoomd lammps-VU lammps-UD
+for ENGINE in cassandra mcccs gomc gromacs hoomd lammps-VU
 do
     if [[ $ENGINE != $1 ]]
     then

diff --git a/reproducibility_project/spe_subproject/src/engine_input/lammps-UD/.keep b/reproducibility_project/spe_subproject/src/engine_input/lammps-UD/.keep
diff --git a/reproducibility_project/spe_subproject/src/engine_input/lammps-UD/in.minimize b/reproducibility_project/spe_subproject/src/engine_input/lammps-UD/in.minimize
diff --git a/reproducibility_project/spe_subproject/src/engine_input/lammps-UD/in.spe b/reproducibility_project/spe_subproject/src/engine_input/lammps-UD/in.spe
diff --git a/reproducibility_project/spe_subproject/src/engine_input/lammps-UD/submit.slurm b/reproducibility_project/spe_subproject/src/engine_input/lammps-UD/submit.slurm
diff --git a/reproducibility_project/spe_subproject/src/engines/lammps-UD/.keep b/reproducibility_project/spe_subproject/src/engines/lammps-UD/.keep
diff --git a/reproducibility_project/spe_subproject/src/engines/lammps-UD/example-project.py b/reproducibility_project/spe_subproject/src/engines/lammps-UD/example-project.py