From 7d759e7583c1cd8858cf8da4ff25032bf063fbcd Mon Sep 17 00:00:00 2001
From: Marc Siggel <marc.siggel@biophys.mpg.de>
Date: Sun, 21 Oct 2018 11:42:07 +0200
Subject: [PATCH 1/4] initial implementation of lammps support

---
 mdbenchmark/generate.py           | 10 +++-
 mdbenchmark/mdengines/__init__.py |  7 +--
 mdbenchmark/mdengines/lammps.py   | 83 +++++++++++++++++++++++++++++++
 mdbenchmark/mdengines/utils.py    |  8 +++
 mdbenchmark/templates/cobra       |  2 +
 mdbenchmark/templates/draco       |  2 +
 mdbenchmark/templates/hydra       |  2 +
 7 files changed, 109 insertions(+), 5 deletions(-)
 create mode 100644 mdbenchmark/mdengines/lammps.py

diff --git a/mdbenchmark/generate.py b/mdbenchmark/generate.py
index dcfb763c..aad41154 100644
--- a/mdbenchmark/generate.py
+++ b/mdbenchmark/generate.py
@@ -31,7 +31,11 @@
     "Parameter paths must be absolute. Only crude file checks are performed! "
     "If you use the {} option make sure you use the GPU compatible NAMD module!"
 )
-
+LAMMPS_WARNING = (
+    "LAMMPS support is experimental."
+    "All input files must be in the same directory and have the same base name!"
+    "We hope you know what you're doing..."
+)
 
 def validate_name(ctx, param, name=None):
     """Validate that we are given a name argument."""
@@ -215,9 +219,11 @@ def generate(name, cpu, gpu, module, host, min_nodes, max_nodes, time, skip_vali
     # click does the validation for us
     template = utils.retrieve_host_template(host)
 
-    # Warn the user that NAMD support is still experimental.
+    # Warn the user that NAMD and LAMMPS support is still experimental.
     if any(["namd" in m for m in module]):
         console.warn(NAMD_WARNING, "--gpu")
+    if any(["lammps" in m for m in module]):
+        console.warn(LAMMPS_WARNING)
 
     module = mdengines.normalize_modules(module, skip_validation)
 
diff --git a/mdbenchmark/mdengines/__init__.py b/mdbenchmark/mdengines/__init__.py
index 1d40e3ff..e2cbe25a 100644
--- a/mdbenchmark/mdengines/__init__.py
+++ b/mdbenchmark/mdengines/__init__.py
@@ -22,10 +22,10 @@
 
 import six
 
-from . import gromacs, namd
+from . import gromacs, namd, lammps
 from .. import console
 
-SUPPORTED_ENGINES = {"gromacs": gromacs, "namd": namd}
+SUPPORTED_ENGINES = {"gromacs": gromacs, "namd": namd, "lammps": lammps}
 
 
 def detect_md_engine(modulename):
@@ -63,6 +63,7 @@ def prepare_module_name(module, skip_validation=False):
                 "--skip-validation",
                 "gromacs/dummy",
                 "namd/dummy",
+                "lammps/dummy"
             )
         console.error("We were not able to determine the module name.")
 
@@ -120,7 +121,7 @@ def normalize_modules(modules, skip_validation):
         if detect_md_engine(engine_name) is None:
             console.error(
                 "There is currently no support for '{}'. "
-                "Supported MD engines are: gromacs, namd.",
+                "Supported MD engines are: gromacs, namd, lammps.",
                 engine_name,
             )
 
diff --git a/mdbenchmark/mdengines/lammps.py b/mdbenchmark/mdengines/lammps.py
new file mode 100644
index 00000000..21a5abb0
--- /dev/null
+++ b/mdbenchmark/mdengines/lammps.py
@@ -0,0 +1,83 @@
+# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
+# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
+#
+# MDBenchmark
+# Copyright (c) 2017 Max Linke & Michael Gecht and contributors
+# (see the file AUTHORS for the full list of names)
+#
+# MDBenchmark is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# MDBenchmark is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with MDBenchmark.  If not, see <http://www.gnu.org/licenses/>.
+import os
+import re
+from glob import glob
+from shutil import copyfile
+
+import mdsynthesis as mds
+import numpy as np
+
+from .. import console
+
+NAME = "lammps"
+
+
+def prepare_benchmark(name, *args, **kwargs):
+    sim = kwargs["sim"]
+
+    full_filename = name + ".in"
+    if name.endswith(".in"):
+        full_filename = name
+        name = name[:-3]
+
+    copyfile(full_filename, sim[full_filename].relpath)
+
+    return name
+
+
+def analyze_lammps_file(fh):
+    """ Check whether the LAMMPS config file has any relative imports or variables
+    """
+    lines = fh.readlines()
+
+    for line in lines:
+        # Continue if we do not need to do anything with the current line
+        if (
+            ("parameters" not in line)
+            and ("coordinates" not in line)
+            and ("structure" not in line)
+        ):
+            continue
+
+        path = line.split()[1]
+        if "$" in path:
+            console.error("Variable Substitutions are not allowed in NAMD files!")
+        if ".." in path:
+            console.error("Relative file paths are not allowed in NAMD files!")
+        if "/" not in path or ("/" in path and not path.startswith("/")):
+            console.error("No absolute path detected in NAMD file!")
+
+
+def check_input_file_exists(name):
+    """Check and append the correct file extensions for the LAMMPS module."""
+    # Check whether the needed files are there.
+    fn = name
+    if fn.endswith(".in"):
+        fn = name[:-4]
+
+    infile = fn + ".in"
+    if not os.path.exists(infile):
+        console.error(
+            "File {} does not exist, but is needed for LAMMPS benchmarks.", infile
+        )
+
+
+    return True
diff --git a/mdbenchmark/mdengines/utils.py b/mdbenchmark/mdengines/utils.py
index 06bee549..cf0e9382 100644
--- a/mdbenchmark/mdengines/utils.py
+++ b/mdbenchmark/mdengines/utils.py
@@ -31,6 +31,7 @@
 FILES_TO_KEEP = {
     "gromacs": [".*/bench\.job", ".*\.tpr", ".*\.mdp"],
     "namd": [".*/bench\.job", ".*\.namd", ".*\.psf", ".*\.pdb"],
+    "lammps": [".*/bench\.job", ".*\.in"],
 }
 
 PARSE_ENGINE = {
@@ -48,6 +49,13 @@
         "ncores_return": lambda line: int(line.split()[3]),
         "analyze": "*out*",
     },
+    "lammps": {
+        "performance": "Performance",
+        "performance_return": lambda line: 1 / float(line.split()[1]),
+        "ncores": "Loop",
+        "ncores_return": lambda line: int(line.split()[5]),
+        "analyze": "*log*",
+    }
 }
 
 
diff --git a/mdbenchmark/templates/cobra b/mdbenchmark/templates/cobra
index 71c03978..c2dfde28 100644
--- a/mdbenchmark/templates/cobra
+++ b/mdbenchmark/templates/cobra
@@ -40,4 +40,6 @@ module load {{ module }}
 srun gmx_mpi mdrun -v -maxh {{ time / 60 }} -deffnm {{ name }}
 {%- elif mdengine == "namd" %}
 srun namd2 {{ name }}.namd
+{%- elif mdengine == "lammps" %}
+srun lmp_mpi -v f tmp.out -l my.log -sc none -i in.alloy
 {%- endif %}
diff --git a/mdbenchmark/templates/draco b/mdbenchmark/templates/draco
index 98f917bb..969ff2fc 100644
--- a/mdbenchmark/templates/draco
+++ b/mdbenchmark/templates/draco
@@ -37,4 +37,6 @@ module load {{ module }}
 srun gmx_mpi mdrun -v -maxh {{ time / 60 }} -deffnm {{ name }}
 {%- elif mdengine == "namd" %}
 srun namd2 {{ name }}.namd
+{%- elif mdengine == "lammps" %}
+srun lmp_mpi -v f tmp.out -l my.log -sc none -i in.alloy
 {%- endif %}
diff --git a/mdbenchmark/templates/hydra b/mdbenchmark/templates/hydra
index f7fbe545..84b9bb61 100644
--- a/mdbenchmark/templates/hydra
+++ b/mdbenchmark/templates/hydra
@@ -23,4 +23,6 @@ module load cuda
 poe gmx_mpi mdrun -deffnm {{ name }} -maxh {{ time / 60 }}
 {%- elif mdengine == "namd" %}
 poe namd2 {{ name }}.namd
+{%- elif mdengine == "lammps" %}
+poe lmp_mpi -v f tmp.out -l my.log -sc none -i {{ name }}.in
 {%- endif %}

From 8c17bb01702bcd6968794fd157cc5535064be4e3 Mon Sep 17 00:00:00 2001
From: Marc Siggel <marc.siggel@biophys.mpg.de>
Date: Sun, 21 Oct 2018 18:06:44 +0200
Subject: [PATCH 2/4] lammps files for tests

---
 .../analyze-files-lammps/.lmps_out.log.swp    | Bin 0 -> 16384 bytes
 ....d9427a82-789d-4789-9186-83e390455fee.json |   1 +
 .../data/analyze-files-lammps/1/bench.job     |  25 +++
 .../tests/data/analyze-files-lammps/1/bulk.in |  90 +++++++++
 .../data/analyze-files-lammps/1/bulk.log      | 178 ++++++++++++++++++
 ....8e48f7fe-5a83-405c-9a4a-0364436ed090.json |   1 +
 .../data/analyze-files-lammps/2/bench.job     |  25 +++
 .../tests/data/analyze-files-lammps/2/bulk.in |  90 +++++++++
 .../2018-10-21_114048.csv                     |   6 +
 ....3b64fda9-fdbe-4a94-b72e-2b97b787e1ab.json |   1 +
 .../data/analyze-files-lammps/3/bench.job     |  25 +++
 .../tests/data/analyze-files-lammps/3/bulk.in |  90 +++++++++
 ....632d511b-03bb-4d1f-b462-d80fdf54d509.json |   1 +
 .../data/analyze-files-lammps/4/bench.job     |  25 +++
 .../tests/data/analyze-files-lammps/4/bulk.in |  90 +++++++++
 ....3aebd58d-893c-4310-addc-60b9f1befa1b.json |   1 +
 .../data/analyze-files-lammps/5/bench.job     |  25 +++
 .../tests/data/analyze-files-lammps/5/bulk.in |  90 +++++++++
 18 files changed, 764 insertions(+)
 create mode 100644 mdbenchmark/tests/data/analyze-files-lammps/.lmps_out.log.swp
 create mode 100644 mdbenchmark/tests/data/analyze-files-lammps/1/Sim.d9427a82-789d-4789-9186-83e390455fee.json
 create mode 100644 mdbenchmark/tests/data/analyze-files-lammps/1/bench.job
 create mode 100644 mdbenchmark/tests/data/analyze-files-lammps/1/bulk.in
 create mode 100644 mdbenchmark/tests/data/analyze-files-lammps/1/bulk.log
 create mode 100644 mdbenchmark/tests/data/analyze-files-lammps/2/Sim.8e48f7fe-5a83-405c-9a4a-0364436ed090.json
 create mode 100644 mdbenchmark/tests/data/analyze-files-lammps/2/bench.job
 create mode 100644 mdbenchmark/tests/data/analyze-files-lammps/2/bulk.in
 create mode 100644 mdbenchmark/tests/data/analyze-files-lammps/2018-10-21_114048.csv
 create mode 100644 mdbenchmark/tests/data/analyze-files-lammps/3/Sim.3b64fda9-fdbe-4a94-b72e-2b97b787e1ab.json
 create mode 100644 mdbenchmark/tests/data/analyze-files-lammps/3/bench.job
 create mode 100644 mdbenchmark/tests/data/analyze-files-lammps/3/bulk.in
 create mode 100644 mdbenchmark/tests/data/analyze-files-lammps/4/Sim.632d511b-03bb-4d1f-b462-d80fdf54d509.json
 create mode 100644 mdbenchmark/tests/data/analyze-files-lammps/4/bench.job
 create mode 100644 mdbenchmark/tests/data/analyze-files-lammps/4/bulk.in
 create mode 100644 mdbenchmark/tests/data/analyze-files-lammps/5/Sim.3aebd58d-893c-4310-addc-60b9f1befa1b.json
 create mode 100644 mdbenchmark/tests/data/analyze-files-lammps/5/bench.job
 create mode 100644 mdbenchmark/tests/data/analyze-files-lammps/5/bulk.in

diff --git a/mdbenchmark/tests/data/analyze-files-lammps/.lmps_out.log.swp b/mdbenchmark/tests/data/analyze-files-lammps/.lmps_out.log.swp
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diff --git a/mdbenchmark/tests/data/analyze-files-lammps/1/Sim.d9427a82-789d-4789-9186-83e390455fee.json b/mdbenchmark/tests/data/analyze-files-lammps/1/Sim.d9427a82-789d-4789-9186-83e390455fee.json
new file mode 100644
index 00000000..6986a04a
--- /dev/null
+++ b/mdbenchmark/tests/data/analyze-files-lammps/1/Sim.d9427a82-789d-4789-9186-83e390455fee.json
@@ -0,0 +1 @@
+{"mdsynthesis": {}, "categories": {"module": "lammps/2016", "gpu": false, "nodes": 1, "host": "draco", "time": 15, "name": "bulk", "started": false}, "tags": []}
\ No newline at end of file
diff --git a/mdbenchmark/tests/data/analyze-files-lammps/1/bench.job b/mdbenchmark/tests/data/analyze-files-lammps/1/bench.job
new file mode 100644
index 00000000..5ed7b7b8
--- /dev/null
+++ b/mdbenchmark/tests/data/analyze-files-lammps/1/bench.job
@@ -0,0 +1,25 @@
+#!/bin/bash -l
+# Standard output and error:
+#SBATCH -o ./bulk.out.%j
+#SBATCH -e ./bulk.err.%j
+# Initial working directory:
+#SBATCH -D ./
+# Job Name:
+#SBATCH -J bulk
+#
+# Queue (Partition):
+#SBATCH --partition=express
+#
+# Number of nodes and MPI tasks per node:
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=32
+# Wall clock limit:
+#SBATCH --time=00:20:00
+
+module purge
+module load impi
+module load cuda
+module load lammps/2016
+
+# Run lammps/2016 for 15 minutes
+srun lmp_mpi -v f tmp.out -l my.log -sc none -i in.alloy
\ No newline at end of file
diff --git a/mdbenchmark/tests/data/analyze-files-lammps/1/bulk.in b/mdbenchmark/tests/data/analyze-files-lammps/1/bulk.in
new file mode 100644
index 00000000..0902db89
--- /dev/null
+++ b/mdbenchmark/tests/data/analyze-files-lammps/1/bulk.in
@@ -0,0 +1,90 @@
+# LAMMPS input script for standardized atomistic simulations
+# Created by emc_setup.pl v2.2.12, July 28, 2017 as part of EMC
+# on Mon Mar  5 16:29:28 CET 2018
+
+# Variable definitions
+
+variable	project		index	"bulk"	# project name
+variable	source		index	.	# data directory
+variable	params		index	.	# parameter directory
+variable	temperature	index	300		# system temperature
+variable	tdamp		index	100.0		# temperature damping
+variable	dielectric	index	1		# medium dielectric
+variable	kappa		index	4		# electrostatics kappa
+variable	cutoff		index	9.5		# standard cutoff
+variable	charge_cutoff	index	9.5		# charge cutoff
+variable	precision	index	0.001		# kspace precision
+variable	lseed		index	723853		# langevin seed
+variable	vseed		index	1486234		# velocity init seed
+variable	tequil		index	1000		# equilibration time
+variable	trun		index	5000  		# run time
+variable	frestart	index	0		# 0: equil, 1: restart
+variable	dtrestart	index	100000		# delta restart time
+variable	dtdump		index	100		# delta dump time
+variable	dtthermo	index	1000		# delta thermo time
+variable	timestep	index	1		# integration time step
+variable	tfreq		index	10		# profile sampling freq
+variable	nsample		index	1000		# profile conf sampling
+variable	dtime		equal	${tfreq}*${nsample}	# profile dtime
+variable	restart		index	${params}/${project}.restart
+
+if "${frestart} != 0" then &
+"variable	data		index	${restart}" &
+else &
+"variable	data		index	${params}/${project}.data" &
+
+# LAMMPS atomistic input script
+
+echo		screen
+units		real
+atom_style	full
+
+# Interaction potential definition
+
+pair_style	lj/class2/coul/long ${cutoff} ${charge_cutoff}
+bond_style	harmonic
+special_bonds	lj/coul 0 0 1
+if "${frestart} != 0" then "read_restart ${data}" else "read_data ${data}"
+include		${params}/${project}.params
+
+# Integration conditions (check)
+
+timestep	${timestep}
+kspace_style	pppm/cg ${precision}
+dielectric	${dielectric}
+fix		mom all momentum 100 linear 1 1 1 angular
+
+# Equilibration
+
+thermo		${dtthermo}
+if "${frestart} != 0" then "jump SELF simulate"
+velocity	all create ${temperature} ${vseed} &
+		dist gaussian rot yes mom yes sum yes
+fix		temp all langevin ${temperature} ${temperature} ${tdamp} &
+		${lseed}
+fix		int all nve/limit 0.1
+run		${tequil}
+unfix		temp
+unfix		int
+write_restart	${project}.restart2
+
+# Simulation
+
+label		simulate
+fix		temp all langevin ${temperature} ${temperature} ${tdamp} &
+		${lseed}
+fix		int all nve
+
+# System sampling: pressure
+
+fix		press all ave/time ${tfreq} ${nsample} ${dtime} &
+		c_thermo_temp &
+		c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &
+		c_thermo_press[4] c_thermo_press[5] c_thermo_press[6] &
+		file ${project}.pressure
+
+# Run conditions
+
+restart		${dtrestart} ${project}.restart1 ${project}.restart2
+dump		1 all custom ${dtdump} ${project}.dump id type x y z
+run		${trun}
diff --git a/mdbenchmark/tests/data/analyze-files-lammps/1/bulk.log b/mdbenchmark/tests/data/analyze-files-lammps/1/bulk.log
new file mode 100644
index 00000000..19a08442
--- /dev/null
+++ b/mdbenchmark/tests/data/analyze-files-lammps/1/bulk.log
@@ -0,0 +1,178 @@
+LAMMPS (11 Aug 2017)
+# LAMMPS input script for standardized atomistic simulations
+# Created by emc_setup.pl v2.2.12, July 28, 2017 as part of EMC
+# on Mon Mar  5 16:29:28 CET 2018
+
+# Variable definitions
+
+variable	project		index	"bulk"	# project name
+variable	source		index	.	# data directory
+variable	params		index	.	# parameter directory
+variable	temperature	index	300		# system temperature
+variable	tdamp		index	100.0		# temperature damping
+variable	dielectric	index	1		# medium dielectric
+variable	kappa		index	4		# electrostatics kappa
+variable	cutoff		index	9.5		# standard cutoff
+variable	charge_cutoff	index	9.5		# charge cutoff
+variable	precision	index	0.001		# kspace precision
+variable	lseed		index	723853		# langevin seed
+variable	vseed		index	1486234		# velocity init seed
+variable	tequil		index	1000		# equilibration time
+variable	trun		index	5000  		# run time
+variable	frestart	index	0		# 0: equil, 1: restart
+variable	dtrestart	index	100000		# delta restart time
+variable	dtdump		index	100		# delta dump time
+variable	dtthermo	index	1000		# delta thermo time
+variable	timestep	index	1		# integration time step
+variable	tfreq		index	10		# profile sampling freq
+variable	nsample		index	1000		# profile conf sampling
+variable	dtime		equal	${tfreq}*${nsample}	# profile dtime
+variable	dtime		equal	10*${nsample}	
+variable	dtime		equal	10*1000	
+variable	restart		index	${params}/${project}.restart
+variable	restart		index	./${project}.restart
+variable	restart		index	./bulk.restart
+
+if "${frestart} != 0" then "variable	data		index	${restart}" else "variable	data		index	${params}/${project}.data"
+variable	data		index	${params}/${project}.data
+variable	data		index	./${project}.data
+variable	data		index	./bulk.data
+# LAMMPS atomistic input script
+
+echo		screen
+  orthogonal box = (0 0 0) to (27.0666 27.0666 27.0666)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  2006 atoms
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  12 = max dihedrals/atom
+  scanning impropers ...
+  4 = max impropers/atom
+  reading bonds ...
+  1586 bonds
+  reading angles ...
+  1930 angles
+  reading dihedrals ...
+  1698 dihedrals
+  reading impropers ...
+  992 impropers
+  4 = max # of 1-2 neighbors
+  7 = max # of 1-3 neighbors
+  11 = max # of special neighbors
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.219179
+  grid = 8 8 8
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.23836
+  estimated relative force accuracy = 0.000717814
+  using double precision FFTs
+  3d grid and FFT values/proc = 2197 512
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 11.5
+  ghost atom cutoff = 11.5
+  binsize = 5.75, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/class2/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  PPPM/cg optimization cutoff: 1e-05
+  Total charged atoms: 100.0%
+  Min/max charged atoms/proc: 100.0% 100.0%
+Per MPI rank memory allocation (min/avg/max) = 16.96 | 16.96 | 16.96 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0          300   -864.06711    348.92602    1277.8162    19231.608 
+    1000    297.11138   -5903.2511    556.92948   -3570.6283    1271.6265 
+Loop time of 22.7831 on 1 procs for 1000 steps with 2006 atoms
+
+Performance: 3.792 ns/day, 6.329 hours/ns, 43.892 timesteps/s
+96.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 17.217     | 17.217     | 17.217     |   0.0 | 75.57
+Bond    | 2.0891     | 2.0891     | 2.0891     |   0.0 |  9.17
+Kspace  | 1.4043     | 1.4043     | 1.4043     |   0.0 |  6.16
+Neigh   | 1.8156     | 1.8156     | 1.8156     |   0.0 |  7.97
+Comm    | 0.11909    | 0.11909    | 0.11909    |   0.0 |  0.52
+Output  | 3.1948e-05 | 3.1948e-05 | 3.1948e-05 |   0.0 |  0.00
+Modify  | 0.11381    | 0.11381    | 0.11381    |   0.0 |  0.50
+Other   |            | 0.02458    |            |       |  0.11
+
+Nlocal:    2006 ave 2006 max 2006 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    10568 ave 10568 max 10568 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    646166 ave 646166 max 646166 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 646166
+Ave neighs/atom = 322.117
+Ave special neighs/atom = 3.50548
+Neighbor list builds = 51
+Dangerous builds = 0
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.219179
+  grid = 8 8 8
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.23836
+  estimated relative force accuracy = 0.000717814
+  using double precision FFTs
+  3d grid and FFT values/proc = 2197 512
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.219179
+  grid = 8 8 8
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.23836
+  estimated relative force accuracy = 0.000717814
+  using double precision FFTs
+  3d grid and FFT values/proc = 2197 512
+Per MPI rank memory allocation (min/avg/max) = 18.29 | 18.29 | 18.29 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+    1000    297.11138   -5903.2511    556.92948   -3570.6283    1271.6265 
+    2000    297.33518   -6022.6452    580.34683   -3665.2675    281.28799 
+    3000    311.72752   -6012.5449    551.38014   -3598.1177   -166.33791 
+    4000    297.91039   -6048.5889    516.69338   -3751.4269   -328.64059 
+    5000    304.90559   -6068.1182     504.4505   -3741.3921    1154.0152 
+    6000    303.58606   -6051.2181    468.16069    -3768.668   -123.65105 
+Loop time of 115.611 on 1 procs for 5000 steps with 2006 atoms
+
+Performance: 3.737 ns/day, 6.423 hours/ns, 43.248 timesteps/s
+94.3% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 88.161     | 88.161     | 88.161     |   0.0 | 76.26
+Bond    | 10.751     | 10.751     | 10.751     |   0.0 |  9.30
+Kspace  | 7.3221     | 7.3221     | 7.3221     |   0.0 |  6.33
+Neigh   | 7.9037     | 7.9037     | 7.9037     |   0.0 |  6.84
+Comm    | 0.58391    | 0.58391    | 0.58391    |   0.0 |  0.51
+Output  | 0.2048     | 0.2048     | 0.2048     |   0.0 |  0.18
+Modify  | 0.55618    | 0.55618    | 0.55618    |   0.0 |  0.48
+Other   |            | 0.129      |            |       |  0.11
+
+Nlocal:    2006 ave 2006 max 2006 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    10643 ave 10643 max 10643 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    645376 ave 645376 max 645376 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 645376
+Ave neighs/atom = 321.723
+Ave special neighs/atom = 3.50548
+Neighbor list builds = 218
+Dangerous builds = 0
+Total wall time: 0:02:18
diff --git a/mdbenchmark/tests/data/analyze-files-lammps/2/Sim.8e48f7fe-5a83-405c-9a4a-0364436ed090.json b/mdbenchmark/tests/data/analyze-files-lammps/2/Sim.8e48f7fe-5a83-405c-9a4a-0364436ed090.json
new file mode 100644
index 00000000..8131c5d1
--- /dev/null
+++ b/mdbenchmark/tests/data/analyze-files-lammps/2/Sim.8e48f7fe-5a83-405c-9a4a-0364436ed090.json
@@ -0,0 +1 @@
+{"mdsynthesis": {}, "categories": {"module": "lammps/2016", "gpu": false, "nodes": 2, "host": "draco", "time": 15, "name": "bulk", "started": false}, "tags": []}
\ No newline at end of file
diff --git a/mdbenchmark/tests/data/analyze-files-lammps/2/bench.job b/mdbenchmark/tests/data/analyze-files-lammps/2/bench.job
new file mode 100644
index 00000000..41573018
--- /dev/null
+++ b/mdbenchmark/tests/data/analyze-files-lammps/2/bench.job
@@ -0,0 +1,25 @@
+#!/bin/bash -l
+# Standard output and error:
+#SBATCH -o ./bulk.out.%j
+#SBATCH -e ./bulk.err.%j
+# Initial working directory:
+#SBATCH -D ./
+# Job Name:
+#SBATCH -J bulk
+#
+# Queue (Partition):
+#SBATCH --partition=express
+#
+# Number of nodes and MPI tasks per node:
+#SBATCH --nodes=2
+#SBATCH --ntasks-per-node=32
+# Wall clock limit:
+#SBATCH --time=00:20:00
+
+module purge
+module load impi
+module load cuda
+module load lammps/2016
+
+# Run lammps/2016 for 15 minutes
+srun lmp_mpi -v f tmp.out -l my.log -sc none -i in.alloy
\ No newline at end of file
diff --git a/mdbenchmark/tests/data/analyze-files-lammps/2/bulk.in b/mdbenchmark/tests/data/analyze-files-lammps/2/bulk.in
new file mode 100644
index 00000000..0902db89
--- /dev/null
+++ b/mdbenchmark/tests/data/analyze-files-lammps/2/bulk.in
@@ -0,0 +1,90 @@
+# LAMMPS input script for standardized atomistic simulations
+# Created by emc_setup.pl v2.2.12, July 28, 2017 as part of EMC
+# on Mon Mar  5 16:29:28 CET 2018
+
+# Variable definitions
+
+variable	project		index	"bulk"	# project name
+variable	source		index	.	# data directory
+variable	params		index	.	# parameter directory
+variable	temperature	index	300		# system temperature
+variable	tdamp		index	100.0		# temperature damping
+variable	dielectric	index	1		# medium dielectric
+variable	kappa		index	4		# electrostatics kappa
+variable	cutoff		index	9.5		# standard cutoff
+variable	charge_cutoff	index	9.5		# charge cutoff
+variable	precision	index	0.001		# kspace precision
+variable	lseed		index	723853		# langevin seed
+variable	vseed		index	1486234		# velocity init seed
+variable	tequil		index	1000		# equilibration time
+variable	trun		index	5000  		# run time
+variable	frestart	index	0		# 0: equil, 1: restart
+variable	dtrestart	index	100000		# delta restart time
+variable	dtdump		index	100		# delta dump time
+variable	dtthermo	index	1000		# delta thermo time
+variable	timestep	index	1		# integration time step
+variable	tfreq		index	10		# profile sampling freq
+variable	nsample		index	1000		# profile conf sampling
+variable	dtime		equal	${tfreq}*${nsample}	# profile dtime
+variable	restart		index	${params}/${project}.restart
+
+if "${frestart} != 0" then &
+"variable	data		index	${restart}" &
+else &
+"variable	data		index	${params}/${project}.data" &
+
+# LAMMPS atomistic input script
+
+echo		screen
+units		real
+atom_style	full
+
+# Interaction potential definition
+
+pair_style	lj/class2/coul/long ${cutoff} ${charge_cutoff}
+bond_style	harmonic
+special_bonds	lj/coul 0 0 1
+if "${frestart} != 0" then "read_restart ${data}" else "read_data ${data}"
+include		${params}/${project}.params
+
+# Integration conditions (check)
+
+timestep	${timestep}
+kspace_style	pppm/cg ${precision}
+dielectric	${dielectric}
+fix		mom all momentum 100 linear 1 1 1 angular
+
+# Equilibration
+
+thermo		${dtthermo}
+if "${frestart} != 0" then "jump SELF simulate"
+velocity	all create ${temperature} ${vseed} &
+		dist gaussian rot yes mom yes sum yes
+fix		temp all langevin ${temperature} ${temperature} ${tdamp} &
+		${lseed}
+fix		int all nve/limit 0.1
+run		${tequil}
+unfix		temp
+unfix		int
+write_restart	${project}.restart2
+
+# Simulation
+
+label		simulate
+fix		temp all langevin ${temperature} ${temperature} ${tdamp} &
+		${lseed}
+fix		int all nve
+
+# System sampling: pressure
+
+fix		press all ave/time ${tfreq} ${nsample} ${dtime} &
+		c_thermo_temp &
+		c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &
+		c_thermo_press[4] c_thermo_press[5] c_thermo_press[6] &
+		file ${project}.pressure
+
+# Run conditions
+
+restart		${dtrestart} ${project}.restart1 ${project}.restart2
+dump		1 all custom ${dtdump} ${project}.dump id type x y z
+run		${trun}
diff --git a/mdbenchmark/tests/data/analyze-files-lammps/2018-10-21_114048.csv b/mdbenchmark/tests/data/analyze-files-lammps/2018-10-21_114048.csv
new file mode 100644
index 00000000..fd863c9f
--- /dev/null
+++ b/mdbenchmark/tests/data/analyze-files-lammps/2018-10-21_114048.csv
@@ -0,0 +1,6 @@
+,module,nodes,ns/day,run time [min],gpu,host,ncores
+0,lammps/2016,1,0.26371308016877637,15,False,draco,1
+1,lammps/2016,2,,15,False,draco,
+2,lammps/2016,3,,15,False,draco,
+3,lammps/2016,4,,15,False,draco,
+4,lammps/2016,5,,15,False,draco,
diff --git a/mdbenchmark/tests/data/analyze-files-lammps/3/Sim.3b64fda9-fdbe-4a94-b72e-2b97b787e1ab.json b/mdbenchmark/tests/data/analyze-files-lammps/3/Sim.3b64fda9-fdbe-4a94-b72e-2b97b787e1ab.json
new file mode 100644
index 00000000..13e2fde4
--- /dev/null
+++ b/mdbenchmark/tests/data/analyze-files-lammps/3/Sim.3b64fda9-fdbe-4a94-b72e-2b97b787e1ab.json
@@ -0,0 +1 @@
+{"mdsynthesis": {}, "categories": {"module": "lammps/2016", "gpu": false, "nodes": 3, "host": "draco", "time": 15, "name": "bulk", "started": false}, "tags": []}
\ No newline at end of file
diff --git a/mdbenchmark/tests/data/analyze-files-lammps/3/bench.job b/mdbenchmark/tests/data/analyze-files-lammps/3/bench.job
new file mode 100644
index 00000000..e5016f2c
--- /dev/null
+++ b/mdbenchmark/tests/data/analyze-files-lammps/3/bench.job
@@ -0,0 +1,25 @@
+#!/bin/bash -l
+# Standard output and error:
+#SBATCH -o ./bulk.out.%j
+#SBATCH -e ./bulk.err.%j
+# Initial working directory:
+#SBATCH -D ./
+# Job Name:
+#SBATCH -J bulk
+#
+# Queue (Partition):
+#SBATCH --partition=express
+#
+# Number of nodes and MPI tasks per node:
+#SBATCH --nodes=3
+#SBATCH --ntasks-per-node=32
+# Wall clock limit:
+#SBATCH --time=00:20:00
+
+module purge
+module load impi
+module load cuda
+module load lammps/2016
+
+# Run lammps/2016 for 15 minutes
+srun lmp_mpi -v f tmp.out -l my.log -sc none -i in.alloy
\ No newline at end of file
diff --git a/mdbenchmark/tests/data/analyze-files-lammps/3/bulk.in b/mdbenchmark/tests/data/analyze-files-lammps/3/bulk.in
new file mode 100644
index 00000000..0902db89
--- /dev/null
+++ b/mdbenchmark/tests/data/analyze-files-lammps/3/bulk.in
@@ -0,0 +1,90 @@
+# LAMMPS input script for standardized atomistic simulations
+# Created by emc_setup.pl v2.2.12, July 28, 2017 as part of EMC
+# on Mon Mar  5 16:29:28 CET 2018
+
+# Variable definitions
+
+variable	project		index	"bulk"	# project name
+variable	source		index	.	# data directory
+variable	params		index	.	# parameter directory
+variable	temperature	index	300		# system temperature
+variable	tdamp		index	100.0		# temperature damping
+variable	dielectric	index	1		# medium dielectric
+variable	kappa		index	4		# electrostatics kappa
+variable	cutoff		index	9.5		# standard cutoff
+variable	charge_cutoff	index	9.5		# charge cutoff
+variable	precision	index	0.001		# kspace precision
+variable	lseed		index	723853		# langevin seed
+variable	vseed		index	1486234		# velocity init seed
+variable	tequil		index	1000		# equilibration time
+variable	trun		index	5000  		# run time
+variable	frestart	index	0		# 0: equil, 1: restart
+variable	dtrestart	index	100000		# delta restart time
+variable	dtdump		index	100		# delta dump time
+variable	dtthermo	index	1000		# delta thermo time
+variable	timestep	index	1		# integration time step
+variable	tfreq		index	10		# profile sampling freq
+variable	nsample		index	1000		# profile conf sampling
+variable	dtime		equal	${tfreq}*${nsample}	# profile dtime
+variable	restart		index	${params}/${project}.restart
+
+if "${frestart} != 0" then &
+"variable	data		index	${restart}" &
+else &
+"variable	data		index	${params}/${project}.data" &
+
+# LAMMPS atomistic input script
+
+echo		screen
+units		real
+atom_style	full
+
+# Interaction potential definition
+
+pair_style	lj/class2/coul/long ${cutoff} ${charge_cutoff}
+bond_style	harmonic
+special_bonds	lj/coul 0 0 1
+if "${frestart} != 0" then "read_restart ${data}" else "read_data ${data}"
+include		${params}/${project}.params
+
+# Integration conditions (check)
+
+timestep	${timestep}
+kspace_style	pppm/cg ${precision}
+dielectric	${dielectric}
+fix		mom all momentum 100 linear 1 1 1 angular
+
+# Equilibration
+
+thermo		${dtthermo}
+if "${frestart} != 0" then "jump SELF simulate"
+velocity	all create ${temperature} ${vseed} &
+		dist gaussian rot yes mom yes sum yes
+fix		temp all langevin ${temperature} ${temperature} ${tdamp} &
+		${lseed}
+fix		int all nve/limit 0.1
+run		${tequil}
+unfix		temp
+unfix		int
+write_restart	${project}.restart2
+
+# Simulation
+
+label		simulate
+fix		temp all langevin ${temperature} ${temperature} ${tdamp} &
+		${lseed}
+fix		int all nve
+
+# System sampling: pressure
+
+fix		press all ave/time ${tfreq} ${nsample} ${dtime} &
+		c_thermo_temp &
+		c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &
+		c_thermo_press[4] c_thermo_press[5] c_thermo_press[6] &
+		file ${project}.pressure
+
+# Run conditions
+
+restart		${dtrestart} ${project}.restart1 ${project}.restart2
+dump		1 all custom ${dtdump} ${project}.dump id type x y z
+run		${trun}
diff --git a/mdbenchmark/tests/data/analyze-files-lammps/4/Sim.632d511b-03bb-4d1f-b462-d80fdf54d509.json b/mdbenchmark/tests/data/analyze-files-lammps/4/Sim.632d511b-03bb-4d1f-b462-d80fdf54d509.json
new file mode 100644
index 00000000..4e5120c9
--- /dev/null
+++ b/mdbenchmark/tests/data/analyze-files-lammps/4/Sim.632d511b-03bb-4d1f-b462-d80fdf54d509.json
@@ -0,0 +1 @@
+{"mdsynthesis": {}, "categories": {"module": "lammps/2016", "gpu": false, "nodes": 4, "host": "draco", "time": 15, "name": "bulk", "started": false}, "tags": []}
\ No newline at end of file
diff --git a/mdbenchmark/tests/data/analyze-files-lammps/4/bench.job b/mdbenchmark/tests/data/analyze-files-lammps/4/bench.job
new file mode 100644
index 00000000..fd6eda85
--- /dev/null
+++ b/mdbenchmark/tests/data/analyze-files-lammps/4/bench.job
@@ -0,0 +1,25 @@
+#!/bin/bash -l
+# Standard output and error:
+#SBATCH -o ./bulk.out.%j
+#SBATCH -e ./bulk.err.%j
+# Initial working directory:
+#SBATCH -D ./
+# Job Name:
+#SBATCH -J bulk
+#
+# Queue (Partition):
+#SBATCH --partition=express
+#
+# Number of nodes and MPI tasks per node:
+#SBATCH --nodes=4
+#SBATCH --ntasks-per-node=32
+# Wall clock limit:
+#SBATCH --time=00:20:00
+
+module purge
+module load impi
+module load cuda
+module load lammps/2016
+
+# Run lammps/2016 for 15 minutes
+srun lmp_mpi -v f tmp.out -l my.log -sc none -i in.alloy
\ No newline at end of file
diff --git a/mdbenchmark/tests/data/analyze-files-lammps/4/bulk.in b/mdbenchmark/tests/data/analyze-files-lammps/4/bulk.in
new file mode 100644
index 00000000..0902db89
--- /dev/null
+++ b/mdbenchmark/tests/data/analyze-files-lammps/4/bulk.in
@@ -0,0 +1,90 @@
+# LAMMPS input script for standardized atomistic simulations
+# Created by emc_setup.pl v2.2.12, July 28, 2017 as part of EMC
+# on Mon Mar  5 16:29:28 CET 2018
+
+# Variable definitions
+
+variable	project		index	"bulk"	# project name
+variable	source		index	.	# data directory
+variable	params		index	.	# parameter directory
+variable	temperature	index	300		# system temperature
+variable	tdamp		index	100.0		# temperature damping
+variable	dielectric	index	1		# medium dielectric
+variable	kappa		index	4		# electrostatics kappa
+variable	cutoff		index	9.5		# standard cutoff
+variable	charge_cutoff	index	9.5		# charge cutoff
+variable	precision	index	0.001		# kspace precision
+variable	lseed		index	723853		# langevin seed
+variable	vseed		index	1486234		# velocity init seed
+variable	tequil		index	1000		# equilibration time
+variable	trun		index	5000  		# run time
+variable	frestart	index	0		# 0: equil, 1: restart
+variable	dtrestart	index	100000		# delta restart time
+variable	dtdump		index	100		# delta dump time
+variable	dtthermo	index	1000		# delta thermo time
+variable	timestep	index	1		# integration time step
+variable	tfreq		index	10		# profile sampling freq
+variable	nsample		index	1000		# profile conf sampling
+variable	dtime		equal	${tfreq}*${nsample}	# profile dtime
+variable	restart		index	${params}/${project}.restart
+
+if "${frestart} != 0" then &
+"variable	data		index	${restart}" &
+else &
+"variable	data		index	${params}/${project}.data" &
+
+# LAMMPS atomistic input script
+
+echo		screen
+units		real
+atom_style	full
+
+# Interaction potential definition
+
+pair_style	lj/class2/coul/long ${cutoff} ${charge_cutoff}
+bond_style	harmonic
+special_bonds	lj/coul 0 0 1
+if "${frestart} != 0" then "read_restart ${data}" else "read_data ${data}"
+include		${params}/${project}.params
+
+# Integration conditions (check)
+
+timestep	${timestep}
+kspace_style	pppm/cg ${precision}
+dielectric	${dielectric}
+fix		mom all momentum 100 linear 1 1 1 angular
+
+# Equilibration
+
+thermo		${dtthermo}
+if "${frestart} != 0" then "jump SELF simulate"
+velocity	all create ${temperature} ${vseed} &
+		dist gaussian rot yes mom yes sum yes
+fix		temp all langevin ${temperature} ${temperature} ${tdamp} &
+		${lseed}
+fix		int all nve/limit 0.1
+run		${tequil}
+unfix		temp
+unfix		int
+write_restart	${project}.restart2
+
+# Simulation
+
+label		simulate
+fix		temp all langevin ${temperature} ${temperature} ${tdamp} &
+		${lseed}
+fix		int all nve
+
+# System sampling: pressure
+
+fix		press all ave/time ${tfreq} ${nsample} ${dtime} &
+		c_thermo_temp &
+		c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &
+		c_thermo_press[4] c_thermo_press[5] c_thermo_press[6] &
+		file ${project}.pressure
+
+# Run conditions
+
+restart		${dtrestart} ${project}.restart1 ${project}.restart2
+dump		1 all custom ${dtdump} ${project}.dump id type x y z
+run		${trun}
diff --git a/mdbenchmark/tests/data/analyze-files-lammps/5/Sim.3aebd58d-893c-4310-addc-60b9f1befa1b.json b/mdbenchmark/tests/data/analyze-files-lammps/5/Sim.3aebd58d-893c-4310-addc-60b9f1befa1b.json
new file mode 100644
index 00000000..8aa5aabe
--- /dev/null
+++ b/mdbenchmark/tests/data/analyze-files-lammps/5/Sim.3aebd58d-893c-4310-addc-60b9f1befa1b.json
@@ -0,0 +1 @@
+{"mdsynthesis": {}, "categories": {"module": "lammps/2016", "gpu": false, "nodes": 5, "host": "draco", "time": 15, "name": "bulk", "started": false}, "tags": []}
\ No newline at end of file
diff --git a/mdbenchmark/tests/data/analyze-files-lammps/5/bench.job b/mdbenchmark/tests/data/analyze-files-lammps/5/bench.job
new file mode 100644
index 00000000..0a8eff54
--- /dev/null
+++ b/mdbenchmark/tests/data/analyze-files-lammps/5/bench.job
@@ -0,0 +1,25 @@
+#!/bin/bash -l
+# Standard output and error:
+#SBATCH -o ./bulk.out.%j
+#SBATCH -e ./bulk.err.%j
+# Initial working directory:
+#SBATCH -D ./
+# Job Name:
+#SBATCH -J bulk
+#
+# Queue (Partition):
+#SBATCH --partition=express
+#
+# Number of nodes and MPI tasks per node:
+#SBATCH --nodes=5
+#SBATCH --ntasks-per-node=32
+# Wall clock limit:
+#SBATCH --time=00:20:00
+
+module purge
+module load impi
+module load cuda
+module load lammps/2016
+
+# Run lammps/2016 for 15 minutes
+srun lmp_mpi -v f tmp.out -l my.log -sc none -i in.alloy
\ No newline at end of file
diff --git a/mdbenchmark/tests/data/analyze-files-lammps/5/bulk.in b/mdbenchmark/tests/data/analyze-files-lammps/5/bulk.in
new file mode 100644
index 00000000..0902db89
--- /dev/null
+++ b/mdbenchmark/tests/data/analyze-files-lammps/5/bulk.in
@@ -0,0 +1,90 @@
+# LAMMPS input script for standardized atomistic simulations
+# Created by emc_setup.pl v2.2.12, July 28, 2017 as part of EMC
+# on Mon Mar  5 16:29:28 CET 2018
+
+# Variable definitions
+
+variable	project		index	"bulk"	# project name
+variable	source		index	.	# data directory
+variable	params		index	.	# parameter directory
+variable	temperature	index	300		# system temperature
+variable	tdamp		index	100.0		# temperature damping
+variable	dielectric	index	1		# medium dielectric
+variable	kappa		index	4		# electrostatics kappa
+variable	cutoff		index	9.5		# standard cutoff
+variable	charge_cutoff	index	9.5		# charge cutoff
+variable	precision	index	0.001		# kspace precision
+variable	lseed		index	723853		# langevin seed
+variable	vseed		index	1486234		# velocity init seed
+variable	tequil		index	1000		# equilibration time
+variable	trun		index	5000  		# run time
+variable	frestart	index	0		# 0: equil, 1: restart
+variable	dtrestart	index	100000		# delta restart time
+variable	dtdump		index	100		# delta dump time
+variable	dtthermo	index	1000		# delta thermo time
+variable	timestep	index	1		# integration time step
+variable	tfreq		index	10		# profile sampling freq
+variable	nsample		index	1000		# profile conf sampling
+variable	dtime		equal	${tfreq}*${nsample}	# profile dtime
+variable	restart		index	${params}/${project}.restart
+
+if "${frestart} != 0" then &
+"variable	data		index	${restart}" &
+else &
+"variable	data		index	${params}/${project}.data" &
+
+# LAMMPS atomistic input script
+
+echo		screen
+units		real
+atom_style	full
+
+# Interaction potential definition
+
+pair_style	lj/class2/coul/long ${cutoff} ${charge_cutoff}
+bond_style	harmonic
+special_bonds	lj/coul 0 0 1
+if "${frestart} != 0" then "read_restart ${data}" else "read_data ${data}"
+include		${params}/${project}.params
+
+# Integration conditions (check)
+
+timestep	${timestep}
+kspace_style	pppm/cg ${precision}
+dielectric	${dielectric}
+fix		mom all momentum 100 linear 1 1 1 angular
+
+# Equilibration
+
+thermo		${dtthermo}
+if "${frestart} != 0" then "jump SELF simulate"
+velocity	all create ${temperature} ${vseed} &
+		dist gaussian rot yes mom yes sum yes
+fix		temp all langevin ${temperature} ${temperature} ${tdamp} &
+		${lseed}
+fix		int all nve/limit 0.1
+run		${tequil}
+unfix		temp
+unfix		int
+write_restart	${project}.restart2
+
+# Simulation
+
+label		simulate
+fix		temp all langevin ${temperature} ${temperature} ${tdamp} &
+		${lseed}
+fix		int all nve
+
+# System sampling: pressure
+
+fix		press all ave/time ${tfreq} ${nsample} ${dtime} &
+		c_thermo_temp &
+		c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &
+		c_thermo_press[4] c_thermo_press[5] c_thermo_press[6] &
+		file ${project}.pressure
+
+# Run conditions
+
+restart		${dtrestart} ${project}.restart1 ${project}.restart2
+dump		1 all custom ${dtdump} ${project}.dump id type x y z
+run		${trun}

From ae8b77344d9814663d28b7d53631013f192d657d Mon Sep 17 00:00:00 2001
From: Marc Siggel <marc.siggel@biophys.mpg.de>
Date: Tue, 23 Oct 2018 09:48:16 +0200
Subject: [PATCH 3/4] added file checks

---
 mdbenchmark/mdengines/lammps.py | 6 +++++-
 mdbenchmark/mdengines/namd.py   | 4 ++++
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/mdbenchmark/mdengines/lammps.py b/mdbenchmark/mdengines/lammps.py
index 21a5abb0..e82f5926 100644
--- a/mdbenchmark/mdengines/lammps.py
+++ b/mdbenchmark/mdengines/lammps.py
@@ -38,7 +38,9 @@ def prepare_benchmark(name, *args, **kwargs):
         full_filename = name
         name = name[:-3]
 
-    copyfile(full_filename, sim[full_filename].relpath)
+    input_file_list = glob("{}*".format(name))
+    for fn in input_file_list:
+        copyfile(full_filename, sim[fn].relpath)
 
     return name
 
@@ -79,5 +81,7 @@ def check_input_file_exists(name):
             "File {} does not exist, but is needed for LAMMPS benchmarks.", infile
         )
 
+    input_files = glob("{}*".format(fn))
+    console.info("The following files will be used to generate the benchmarks:\n {}", ", ".join(input_files))
 
     return True
diff --git a/mdbenchmark/mdengines/namd.py b/mdbenchmark/mdengines/namd.py
index d369c125..70681b23 100644
--- a/mdbenchmark/mdengines/namd.py
+++ b/mdbenchmark/mdengines/namd.py
@@ -77,6 +77,7 @@ def analyze_namd_file(fh):
 def check_input_file_exists(name):
     """Check and append the correct file extensions for the NAMD module."""
     # Check whether the needed files are there.
+    input_files = []
     for extension in ["namd", "psf", "pdb"]:
         if name.endswith(".{}".format(extension)):
             name = name[: -2 + len(extension)]
@@ -86,5 +87,8 @@ def check_input_file_exists(name):
             console.error(
                 "File {} does not exist, but is needed for NAMD benchmarks.", fn
             )
+        input_files.append(fn)
+
+    console.info("The following files will be used to generate the benchmarks: {}", ", ".join(input_files))
 
     return True

From dbecd19d2bc11ec080419c6d40dbf44c8fc54622 Mon Sep 17 00:00:00 2001
From: Marc Siggel <marc.siggel@biophys.mpg.de>
Date: Tue, 23 Oct 2018 10:51:27 +0200
Subject: [PATCH 4/4] updated lammps file checks

---
 mdbenchmark/mdengines/lammps.py | 23 -----------------------
 1 file changed, 23 deletions(-)

diff --git a/mdbenchmark/mdengines/lammps.py b/mdbenchmark/mdengines/lammps.py
index e82f5926..683e7aa7 100644
--- a/mdbenchmark/mdengines/lammps.py
+++ b/mdbenchmark/mdengines/lammps.py
@@ -45,29 +45,6 @@ def prepare_benchmark(name, *args, **kwargs):
     return name
 
 
-def analyze_lammps_file(fh):
-    """ Check whether the LAMMPS config file has any relative imports or variables
-    """
-    lines = fh.readlines()
-
-    for line in lines:
-        # Continue if we do not need to do anything with the current line
-        if (
-            ("parameters" not in line)
-            and ("coordinates" not in line)
-            and ("structure" not in line)
-        ):
-            continue
-
-        path = line.split()[1]
-        if "$" in path:
-            console.error("Variable Substitutions are not allowed in NAMD files!")
-        if ".." in path:
-            console.error("Relative file paths are not allowed in NAMD files!")
-        if "/" not in path or ("/" in path and not path.startswith("/")):
-            console.error("No absolute path detected in NAMD file!")
-
-
 def check_input_file_exists(name):
     """Check and append the correct file extensions for the LAMMPS module."""
     # Check whether the needed files are there.