| Next changeset 1:afcb925def69 (2020-11-13) |
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Commit message:
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827" |
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added:
NEQGamma.py NEQGamma.xml get_clusters.py rmsd_clustering.py test-data/NEQGamma_clusters.json test-data/NEQGamma_ofrict.txt test-data/NEQGamma_ofrict1.txt test-data/NEQGamma_ofrict2.txt test-data/NEQGamma_outp.txt test-data/NEQGamma_outp1.txt test-data/NEQGamma_outp2.txt test-data/Z.tabular test-data/clusters.json test-data/contacts.dat test-data/contacts2.dat test-data/cov.dat test-data/dendrogram.png test-data/heatmap.png test-data/inp.json test-data/outp.txt test-data/outp_mat.tabular test-data/output.json test-data/proj.dat test-data/proj2.dat test-data/pull1.xvg test-data/pull2.xvg test-data/pull3.xvg test-data/stats.dat test-data/traj_cut.dcd test-data/val.dat test-data/val2.dat test-data/vec.dat |
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| diff -r 000000000000 -r 4f3222cb5cf6 NEQGamma.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NEQGamma.py Fri Sep 11 21:54:45 2020 +0000 |
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| b'@@ -0,0 +1,210 @@\n+#!/usr/bin/env python\n+\n+# coding: utf-8\n+# This script is a modified version of a script written\n+# by Steffen Wolf under the GPL v3.0.\n+# The original version can be accessed at\n+# https://github.com/moldyn/dcTMD/blob/master/NEQGamma.py\n+\n+import argparse\n+import json\n+import sys\n+\n+import numpy as np\n+\n+import pandas as pd\n+\n+import scipy\n+import scipy.integrate\n+from scipy.ndimage.filters import gaussian_filter\n+\n+\n+def get_file_names(list_file):\n+ with open(list_file) as f:\n+ return [line for line in f.read().split(\'\\n\') if line]\n+\n+\n+def NEQGamma(file_names, output, output_frict, vel, T, av, sigma):\n+ N = len(file_names)\n+ RT = 0.0083144598 * T\n+\n+ sys.stdout.write("reading data...\\n")\n+\n+ # read in initial data to get length of necessary array\n+ test_file = pd.read_csv(file_names[0], delim_whitespace=True,\n+ header=None, skiprows=17, dtype=float)\n+ length_data = len(test_file[0].values)\n+ full_force_set = np.zeros((N, length_data))\n+ x = np.zeros(length_data)\n+ t = np.zeros(length_data)\n+ t = test_file[0].values\n+ x = test_file[0].values * vel\n+\n+ # read in data\n+ for i in range(0, N):\n+ current_file_name = file_names[i]\n+ sys.stdout.write("reading file {}\\n".format(current_file_name))\n+ input_file_data = pd.read_csv(current_file_name, delim_whitespace=True,\n+ header=None, skiprows=17, dtype=float)\n+ full_force_set[i, :] = input_file_data[1].values\n+\n+ # preprocessing\n+ # * force average: calculate $\\left< f_c (t)\\right>_N$.\n+ # **Important:** this is an ensemble average over the trajectory ensemble\n+ # $N$, not the time average over $t$\n+ av_force = np.zeros(length_data)\n+ av_forceintegral = np.zeros(length_data)\n+ for i in range(length_data):\n+ av_force[i] = np.mean(full_force_set[:, i])\n+ av_forceintegral[1:] = scipy.integrate.cumtrapz(av_force, x)\n+\n+ # calculate $\\delta f_c(t) = f_c(t) - \\left< f_c (t) \\right>_N$ for all $t$\n+ sys.stdout.write("calculating fluctuations...\\n")\n+ delta_force_set = np.zeros((N, length_data))\n+ for i in range(length_data):\n+ delta_force_set[:, i] = full_force_set[:, i] - av_force[i]\n+\n+ # evaluation\n+ # * optimized algorithm for numerical evaluation:\n+ # * integrate: $\\int_0^t dt\' \\delta f_c(t\')$ for all $t\'$\n+ # * multiply by $\\delta f_c(t)$ to yield\n+ # $\\int_0^t dt\'\\delta f_c(t) \\delta f_c(t\')$ for $t$\n+ # with all $t\' \\leq t$ each\n+ # * then calculate the ensemble average\n+ # $\\left< \\int_0^t dt\' \\delta f_c(t) \\delta f_c(t\') \\right>$\n+ int_delta_force_set = np.zeros((N, length_data))\n+ for n in range(N):\n+ int_delta_force_set[n, 1:] = scipy.integrate.cumtrapz(\n+ delta_force_set[n, :], t)\n+\n+ sys.stdout.write("averaging and integrating...\\n")\n+ intcorr = np.zeros((N, length_data))\n+\n+ for n in range(N):\n+ for i in range(length_data):\n+ intcorr[n, i] = delta_force_set[n, i] * int_delta_force_set[n, i]\n+ if i % 1000 == 0:\n+ sys.stdout.write("Trajectory {:2d} {:3.1f} % done\\r".format(\n+ n + 1, (i / length_data) * 100))\n+\n+ # shape of $\\int_0^t dt\' \\delta f_c(t) \\delta f_c(t\')$:\n+ sys.stdout.write("final average...\\n")\n+ av_intcorr = np.zeros(length_data)\n+ for i in range(length_data):\n+ av_intcorr[i] = np.mean(intcorr[:, i]) / RT\n+\n+ # autocorrelation function evaluation:\n+ # * calculate $\\left< \\delta f_c(t) \\delta f_c(t\') \\right>$\n+ # for the last $t$\n+\n+ corr_set = np.zeros((N, length_data))\n+ autocorr_set = np.zeros(length_data)\n+\n+ sys.stdout.write("calculating and processing ACF...\\n")\n+ for n in range(N):\n+ for i in range(length_data):\n+ corr_set[n, i] = delta_force_set[\n+ n, i] * delta_force_set[n, length_data - 1]\n+\n+ for i in range(len'..b'_force_integral\\n")\n+ for i in range(length_data):\n+ dist.write("{:15.8f} {:20.8f} {:20.8f} {:20.8f} {:20.8f}\\n".format(\n+ x[i], av_forceintegral[i], av_intcorr[i], wdiss[i],\n+ av_forceintegral[i] - wdiss[i]))\n+\n+ frict.write("""#x ACF frict_coeff """\n+ """gauss_filtered_frict_coeff av_window_frict_coeff\\n""")\n+ for i in range(length_data):\n+ frict.write("{:15.8f} {:20.8f} {:20.8f} {:20.8f} {:20.8f}\\n".format(\n+ x[i], autocorr_set[i], av_intcorr[i], blurred[i], runn_av[i]))\n+\n+ dist.close()\n+ frict.close()\n+\n+ sys.stdout.write("Done!\\n")\n+\n+\n+def main():\n+ parser = argparse.ArgumentParser(description="""dcTMD friciton correction\n+ (please cite: Wolf, S., Stock, G. Targeted Molecular Dynamics\n+ Calculations of Free Energy Profiles Using a Nonequilibrium\n+ Friction Correction. J. Chem. Theory Comput. 2018, 14(12), 6175-6182,\n+ DOI: 10.1021/acs.jctc.8b00835). Integrates a constraint force file via\n+ trapezoid rule, calculates the NEQ memory friction kernel and friction\n+ factors, and performs a friction correction. First column: reaction\n+ coordinate in nm calculated via t * vel. Second column: force integral,\n+ i.e. the work profile. Third column: friction factors. Fourth column:\n+ trapezoid integral (final value) of friction work along reaction\n+ coordinate. Fourth column: friction corrected work profile. ATTENTION:\n+ Use with python3 or higher!""")\n+ parser.add_argument(\'-i\', metavar=\'<xvg force file>\', type=str,\n+ help="""List of xvg constraint force files prefix\n+ as given by Gromacs mdrun -pf option before running\n+ number.""")\n+ parser.add_argument(\'-o\', metavar=\'<combined results>\', type=str,\n+ help="""file to write x, dG(x), friction coefficeint by\n+ integration (time resolved), and the friction-corrected\n+ dG(x).""")\n+ parser.add_argument(\'-ofrict\', metavar=\'<combined friction results>\',\n+ type=str,\n+ help="""file to write x, ACF, friction coefficeint by\n+ integration (time resolved), gauss filtered friction\n+ coefficient, and slide window averaged friction.""")\n+ parser.add_argument(\'-vel\', metavar=\'<pull velocity>\', type=float,\n+ help="""pull velocity in nm/ps for converting simulation\n+ time t into distance x""")\n+ parser.add_argument(\'-T\', metavar=\'<temperature>\', type=float,\n+ help=\'temperature in K\')\n+ parser.add_argument(\'-av\', metavar=\'<average window>\', type=int,\n+ help="""size of averaging window for displaying\n+ Gamma(x) (recommended: 4 to 20 per 100 data points)""")\n+ parser.add_argument(\'-sigma\', metavar=\'<gauss blurr>\', type=int,\n+ help="""sigma value for Gauss filter for displaying\n+ Gamma(x) (recommended: 4 per 100 data points)""")\n+ parser.add_argument(\'-json\', metavar=\'<json>\', type=str,\n+ help=\'JSON file defining cluster membership\')\n+\n+ args = parser.parse_args()\n+\n+ file_names = get_file_names(args.i)\n+ if args.json:\n+ with open(args.json) as f:\n+ j = json.load(f)\n+ file_names_dct = {n: [file_names[int(m)] for m in j[n]] for n in j}\n+\n+ for cluster in file_names_dct:\n+ NEQGamma(file_names_dct[cluster],\n+ \'cluster{}_{}\'.format(cluster, args.o),\n+ \'cluster{}_{}\'.format(cluster, args.ofrict),\n+ args.vel, args.T, args.av, args.sigma)\n+ else:\n+ NEQGamma(file_names, args.o, args.ofrict, args.vel,\n+ args.T, args.av, args.sigma)\n+\n+\n+if __name__ == "__main__":\n+ main()\n' |
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| diff -r 000000000000 -r 4f3222cb5cf6 NEQGamma.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NEQGamma.xml Fri Sep 11 21:54:45 2020 +0000 |
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| @@ -0,0 +1,125 @@ +<tool id="biomd_neqgamma" name="dcTMD friction correction" version="0.@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> + <description>for calculating friction and free energy profiles from TMD ensembles</description> + <macros> + <token name="@TOOL_VERSION@">1.5.2</token> + <token name="@VERSION_SUFFIX@">0</token> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">scipy</requirement> + <requirement type="package" version="1.19.1">numpy</requirement> + <requirement type="package" version="1.1.2">pandas</requirement> + </requirements> + <command><![CDATA[ + #for t in $xvgs: + echo $t &>> ./xvgs.txt && + #end for + + python '$__tool_directory__/NEQGamma.py' + -i ./xvgs.txt + -o outp.txt + -ofrict ofrict.txt + -vel '$vel' + -T '$T' + -av '$av' + -sigma '$sigma' + #if $json: + -json '$json' + #end if + + ]]></command> + <inputs> + <param type="data_collection" name="xvgs" label="XVG constraint force files" format="xvg" help="XVG files generated by GROMACS"/> + <param type="data" name="json" optional="true" label="Ensemble subgroups" format="json" help="Optional: list of sub-ensembles in JSON format (e.g. produced by the 'Extract clusters' tool). If not specified, results will be calculated for the entire ensemble."/> + <param label="Pull velocity in nm/ps of the TMD simulations" value="0.001" min="0" type="float" name="vel" argument="-vel"/> + <param label="Temperature in K" value="300" min="0" type="float" name="T" argument="-T"/> + <param label="Size of averaging window for displaying Gamma(x)" value="0" min="0" type="integer" name="av" argument="-av" help="Recommended: 4 to 20 per 100 data points."/> + <param label="Sigma value for Gauss filter for displaying Gamma(x)" value="0" min="0" type="integer" name="sigma" argument="-sigma" help="Recommended: 4 per 100 data points."/> + </inputs> + <outputs> + <collection name="outp_col" type="list" label="Free energy data"> + <discover_datasets pattern="(?P<designation>^cluster\d+)_outp\.txt$" ext="txt"/> + <filter>json</filter> + </collection> + <collection name="outp_frict_col" type="list" label="Friction data"> + <discover_datasets pattern="(?P<designation>^cluster\d+)_ofrict\.txt$" ext="txt"/> + <filter>json</filter> + </collection> + <data name="outp" from_work_dir="outp.txt" format="tabular" label="Free energy data"> + <filter>not json</filter> + </data> + <data name="outp_frict" from_work_dir="ofrict.txt" format="tabular" label="Friction data"> + <filter>not json</filter> + </data> + </outputs> + <tests> + <test> + <param name="xvgs"> + <collection type="list"> + <element name="pull1" ftype="xvg" value="pull1.xvg" /> + <element name="pull2" ftype="xvg" value="pull2.xvg" /> + <element name="pull3" ftype="xvg" value="pull3.xvg" /> + </collection> + </param> + <param name="vel" value="0.001" /> + <param name="T" value="300" /> + <param name="av" value="20" /> + <param name="sigma" value="20" /> + <output name="outp" value="NEQGamma_outp.txt" /> + <output name="outp_frict" value="NEQGamma_ofrict.txt" /> + </test> + <test> + <param name="xvgs"> + <collection type="list"> + <element name="pull1" ftype="xvg" value="pull1.xvg" /> + <element name="pull2" ftype="xvg" value="pull2.xvg" /> + <element name="pull3" ftype="xvg" value="pull3.xvg" /> + </collection> + </param> + <param name="json" value="NEQGamma_clusters.json" /> + <param name="vel" value="0.001" /> + <param name="T" value="300" /> + <param name="av" value="20" /> + <param name="sigma" value="20" /> + <output_collection name="outp_col" type="list"> + <element name="cluster0" file="NEQGamma_outp1.txt"/> + <element name="cluster1" file="NEQGamma_outp2.txt"/> + </output_collection> + <output_collection name="outp_frict_col" type="list"> + <element name="cluster0" file="NEQGamma_ofrict1.txt"/> + <element name="cluster1" file="NEQGamma_ofrict2.txt"/> + </output_collection> + </test> + + </tests> + <help><![CDATA[ + +.. class:: infomark + +**What it does** + +Perform dcTMD friction correction from an ensemble of XVG files generated by GROMACS targeted molecular dynamics (TMD) simulations. + +_____ + + +.. class:: infomark + +**Input** + + - Ensemble of XVG files from TMD simulations + - Optional: JSON file containing subgroups of trajectories from the ensemble. If this option is used, the dcTMD calculation will be performed separately for each sub-ensemble. + +_____ + + +.. class:: infomark + +**Output** + + - Tab-separated files containing free energy and friction data. +]]></help> + <citations> + <citation type="doi">10.1021/acs.jctc.8b00835</citation> + </citations> +</tool> + |
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| diff -r 000000000000 -r 4f3222cb5cf6 get_clusters.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_clusters.py Fri Sep 11 21:54:45 2020 +0000 |
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| @@ -0,0 +1,39 @@ +import argparse +import collections +import json + +import numpy as np + +from scipy.cluster.hierarchy import fcluster + + +def separate_clusters(Z_fpath, threshold, min_members, output): + Z = np.loadtxt(Z_fpath) + branch_assignments = fcluster(Z, threshold, criterion='distance') + cluster_dict = collections.defaultdict(list) + for n, val in enumerate(branch_assignments): + cluster_dict[branch_assignments[n]].append(n) + cluster_dict = {int(k): v for k, v in cluster_dict.items() + if len(v) >= min_members} + with open(output, 'w') as f: + json.dump(cluster_dict, f, indent=4, sort_keys=True) + + +def main(): + parser = argparse.ArgumentParser() + parser.add_argument('--Z', required=True, + help='File for cluster linkage array.') + parser.add_argument('--threshold', type=int, required=True, + help='Distance cutoff.') + parser.add_argument('--min-members', type=int, required=True, + help='Minimum number of members of the cluster.') + parser.add_argument('--output', required=True, + help='Output file.') + args = parser.parse_args() + + separate_clusters(args.Z, args.threshold, + args.min_members, args.output) + + +if __name__ == "__main__": + main() |
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| diff -r 000000000000 -r 4f3222cb5cf6 rmsd_clustering.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rmsd_clustering.py Fri Sep 11 21:54:45 2020 +0000 |
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| @@ -0,0 +1,114 @@ +import argparse +import json + +import matplotlib.pyplot as plt + +import numpy as np + +from scipy.cluster.hierarchy import cophenet, dendrogram, linkage +from scipy.spatial.distance import pdist + + +def json_to_np(fname, start=None, end=None): + """ + Load json file and convert to numpy array + """ + with open(fname) as f: + k = json.load(f) + print(np.array(k)[:, :, start:end].shape) + return np.array(k)[:, :, start:end] + + +def flatten_tensor(tensor, normalize=True): + """ + Flatten tensor to a 2D matrix along the time axis + """ + av = np.mean(tensor, axis=(0, 1)) if normalize else 1 + return np.mean(tensor/av, axis=2) + + +def get_cluster_linkage_array(mat, clustering_method='average'): + Z = linkage(mat, clustering_method) + c, coph_dists = cophenet(Z, pdist(mat)) + print('Cophenetic correlation coefficient: {}'.format(c)) + return Z + + +def plot_dist_mat(mat, output, cmap='plasma'): + """ + Plot distance matrix as heatmap + """ + fig, ax = plt.subplots(1) + p = ax.pcolormesh(mat, cmap=cmap) + plt.xlabel('Trajectory number') + plt.ylabel('Trajectory number') + plt.colorbar(p) + plt.draw() + plt.savefig(output, format='png') + + +def plot_dendrogram(Z, output): + plt.figure(figsize=(25, 10)) + plt.title('Hierarchical Clustering Dendrogram') + plt.xlabel('Trajectory index') + plt.ylabel('distance') + dendrogram( + Z, + leaf_rotation=90., # rotates the x axis labels + leaf_font_size=8., # font size for the x axis labels + ) + plt.savefig(output, format='png') + + +def main(): + parser = argparse.ArgumentParser() + parser.add_argument('--json', help='JSON input file (for 3D tensor).') + parser.add_argument('--mat', help='Input tabular file (for 2D matrix).') + parser.add_argument('--outp-mat', help='Tabular output file.') + parser.add_argument('--Z', required=True, + help='File for cluster linkage array.') + parser.add_argument('--dendrogram', + help="Path to the output dendrogram file") + parser.add_argument('--heatmap', + help="Path to the output distance matrix file") + parser.add_argument('--clustering-method', default='average', + choices=['single', 'complete', 'average', + 'centroid', 'median', 'ward', 'weighted'], + help="Method to use for clustering.") + parser.add_argument('--cmap', type=str, default='plasma', + help="Matplotlib colormap to use" + "for plotting distance matrix.") + parser.add_argument('--start', type=int, + help="First trajectory frame to" + "calculate distance matrix") + parser.add_argument('--end', type=int, + help="Last trajectory frame to" + "calculate distance matrix") + parser.add_argument('--normalize', action="store_true", + help="Normalize the RMSD variation over" + "the trajectories before averaging.") + args = parser.parse_args() + + print(args) + if args.json: + tensor = json_to_np(args.json, args.start, args.end) + mat = flatten_tensor(tensor, args.normalize) + np.savetxt(args.outp_mat, mat) + elif args.mat: + mat = np.loadtxt(args.mat) + else: + print("Either --json or --mat must be specified.") + exit(1) + + Z = get_cluster_linkage_array(mat, args.clustering_method) + np.savetxt(args.Z, Z) + + if args.heatmap: + plot_dist_mat(mat, args.heatmap, args.cmap) + + if args.dendrogram: + plot_dendrogram(Z, args.dendrogram) + + +if __name__ == "__main__": + main() |
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| diff -r 000000000000 -r 4f3222cb5cf6 test-data/NEQGamma_clusters.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NEQGamma_clusters.json Fri Sep 11 21:54:45 2020 +0000 |
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| @@ -0,0 +1,1 @@ +{"0": ["0", "1"], "1": ["0", "2"]} |
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| diff -r 000000000000 -r 4f3222cb5cf6 test-data/NEQGamma_ofrict.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NEQGamma_ofrict.txt Fri Sep 11 21:54:45 2020 +0000 |
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| b'@@ -0,0 +1,102 @@\n+#x ACF frict_coeff gauss_filtered_frict_coeff av_window_frict_coeff\n+ 0.00000000 439653.22756622 0.00000000 39.85704130 -164.30975524\n+ 0.00000200 41861.51118060 -309.80490686 39.90128147 -42.50284457\n+ 0.00000400 -4760.58383990 -1433.31122481 39.98937507 132.75776205\n+ 0.00000600 -52063.97568219 -1302.42266399 40.10796653 273.24484877\n+ 0.00000800 -94137.43307581 -696.00283593 40.26787861 322.90057440\n+ 0.00001000 -109240.44374298 59.67135417 40.47438205 310.49706801\n+ 0.00001200 -91296.29474097 200.26534006 40.74119359 300.71687201\n+ 0.00001400 -42279.73264591 -211.00314767 41.08344474 307.77939795\n+ 0.00001600 29083.13222726 -299.86397145 41.51045417 289.59363364\n+ 0.00001800 100957.95082594 706.27695160 42.02391473 213.62523715\n+ 0.00002000 150492.32652407 2436.13821354 42.62185633 115.80351000\n+ 0.00002200 163610.52308989 3505.21213240 43.30185229 72.52474633\n+ 0.00002400 137798.21546909 2809.74173435 44.06395945 119.32042200\n+ 0.00002600 86552.97296922 993.11451262 44.91354630 219.23877027\n+ 0.00002800 30065.89230936 -248.07012791 45.85833909 214.16642537\n+ 0.00003000 -15271.83960767 -195.60392001 46.90428227 107.42336841\n+ 0.00003200 -41143.37576909 141.25051892 48.05595140 -10.23715919\n+ 0.00003400 -45603.75654834 -363.71528632 49.31891708 -41.13071129\n+ 0.00003600 -31933.14574422 -1519.36792976 50.67717643 11.13789839\n+ 0.00003800 -11580.24564270 -1956.43454302 52.14035913 47.86749694\n+ 0.00004000 1795.96943076 -865.57527338 53.69638462 -13.42971260\n+ 0.00004200 -6069.40567724 626.10860652 55.34660090 -151.70147237\n+ 0.00004400 -36605.44103603 565.05574074 57.08967355 -284.06117371\n+ 0.00004600 -88409.03954732 -1403.86956218 58.91185508 -352.46208669\n+ 0.00004800 -119187.64656330 -2830.86397506 60.79652934 -358.13736161\n+ 0.00005000 -126958.63383213 -2293.53919791 62.72537859 -329.02117947\n+ 0.00005200 -105144.23378691 -417.60570188 64.67974189 -286.64057459\n+ 0.00005400 -57578.18477311 834.36904591 66.64059843 -231.16675138\n+ 0.00005600 7642.76668942 434.72799961 68.58976595 -160.41908396\n+ 0.00005800 73314.58537446 -519.66723923 70.51136345 -97.11322986\n+ 0.00006000 117239.42596973 -329.29698187 72.38916035 -71.95507125\n+ 0.00006200 122335.84589389 858.01810556 74.20116994 -72.69735215\n+ 0.00006400 90700.59252948 1441.72347492 75.92201577 -50.06936146\n+ 0.00006600 40928.26316446 879.60901414 77.52654008 55.63484244\n+ 0.00006800 -3181.66487546 334.25351485 78.99192675 197.17614864\n+ 0.00007000 -31227.72623817 652.00817770 80.29696328 378.84255238\n+ 0.00007200 -43642.08135556 1250.72698300 81.42019653 507.21229626\n+ 0.00007400 -37578.91493866 1051.23806218 82.34208812 533.01944777\n+ 0.00007600 -9313.59450148 -253.25084775 '..b' 2216.16123424 47.49918918 -248.93156307\n+ 0.00012400 63226.50291119 2740.29495857 46.05677747 -270.24081648\n+ 0.00012600 7112.67333129 642.99155129 44.93086250 -206.96775261\n+ 0.00012800 4737.67676382 673.17973142 44.16608448 -50.37244372\n+ 0.00013000 -10629.83066809 -276.05014319 43.80477020 154.04681427\n+ 0.00013200 -24445.08596782 -1331.11596207 43.87860095 320.32723893\n+ 0.00013400 -38089.44576760 -2042.60347448 44.40990189 378.66585808\n+ 0.00013600 -53888.48385453 -2339.54888278 45.42258092 320.31441637\n+ 0.00013800 -65525.93331796 -2263.02943488 46.94717499 192.76961767\n+ 0.00014000 -66605.80950981 -1978.10144773 49.01173919 46.49351043\n+ 0.00014200 -59461.87405093 -1395.88433631 51.62964197 -100.43225450\n+ 0.00014400 -50082.83777468 -136.33782409 54.79891493 -258.31822307\n+ 0.00014600 -36265.73051644 1692.89613965 58.50910094 -447.27992440\n+ 0.00014800 -11065.11218743 2974.81823090 62.74931610 -601.98154580\n+ 0.00015000 24574.77396976 2642.88373319 67.50830566 -716.60080679\n+ 0.00015200 53704.30727291 913.24280375 72.76914377 -754.65637852\n+ 0.00015400 62641.21173742 -927.03460327 78.50486320 -713.36174226\n+ 0.00015600 50475.22167026 -1689.34471443 84.67941051 -602.77004154\n+ 0.00015800 27415.48879178 -1332.07133205 91.25069147 -429.82867913\n+ 0.00016000 659.52027909 -793.99131765 98.16114225 -214.90982911\n+ 0.00016200 -27358.17056213 -941.55813718 105.35683648 -1.93703392\n+ 0.00016400 -36359.81639946 -1038.93906805 112.78930315 141.63166343\n+ 0.00016600 -103478.83628142 -2451.04087672 120.41222030 155.07119820\n+ 0.00016800 -98122.08801466 -1619.20548854 128.15466148 39.58301004\n+ 0.00017000 -91470.31369949 -1037.16157762 135.94071127 -128.72347744\n+ 0.00017200 -70167.76251890 -505.22323695 143.69516807 -240.17685720\n+ 0.00017400 -43298.45234300 169.23053990 151.35171103 -223.11938998\n+ 0.00017600 -13147.13005351 1119.27836540 158.84649112 -87.45006406\n+ 0.00017800 13812.88135432 2035.34756564 166.10612536 85.27603300\n+ 0.00018000 29405.90836664 2281.35445610 173.04701036 209.91332866\n+ 0.00018200 27785.78282904 1475.48961051 179.59291666 253.65425754\n+ 0.00018400 16400.24253711 132.45287134 185.68841711 300.73216440\n+ 0.00018600 5032.51740518 -616.86762340 191.28914198 352.67911780\n+ 0.00018800 -684.42414340 -391.31151887 196.34017758 475.23116164\n+ 0.00019000 -2606.74806622 413.81613798 200.77390679 556.19143606\n+ 0.00019200 -4228.75142469 1254.39214820 204.53041970 608.04951495\n+ 0.00019400 -2944.53596867 1786.35191510 207.57544804 633.31067679\n+ 0.00019600 4064.05842526 1765.17722675 209.89395091 624.84914980\n+ 0.00019800 11878.81314410 1160.67458116 211.46967661 568.88523153\n+ 0.00020000 12188.47862387 80.82726004 212.27097983 467.11785325\n' |
| b |
| diff -r 000000000000 -r 4f3222cb5cf6 test-data/NEQGamma_ofrict1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NEQGamma_ofrict1.txt Fri Sep 11 21:54:45 2020 +0000 |
| b |
| b'@@ -0,0 +1,102 @@\n+#x ACF frict_coeff gauss_filtered_frict_coeff av_window_frict_coeff\n+ 0.00000000 -131993.41016925 0.00000000 -31.41159270 -71.62375840\n+ 0.00000200 16345.04469682 -1345.26646099 -31.23092179 16.85099383\n+ 0.00000400 29113.39120702 -1454.28761686 -30.88206666 43.12225366\n+ 0.00000600 27656.43517472 -264.14035591 -30.38447804 -24.61744170\n+ 0.00000800 22081.05883970 570.71230720 -29.75116213 -124.82229209\n+ 0.00001000 9926.50084650 482.67878751 -28.98362546 -148.88674802\n+ 0.00001200 -5957.22964270 -306.50010800 -28.07154561 -44.25804572\n+ 0.00001400 -21071.08253355 -678.79838871 -27.00311927 120.09671342\n+ 0.00001600 -30206.93805045 129.24578885 -25.77749754 210.63856614\n+ 0.00001800 -30292.41328536 1433.88087902 -24.40797512 147.07777675\n+ 0.00002000 -21089.95150080 1769.49504443 -22.91494801 -14.98005248\n+ 0.00002200 -5123.22129025 525.42519661 -21.31752461 -139.14697408\n+ 0.00002400 14086.19434495 -1354.79390711 -19.63003766 -71.97480155\n+ 0.00002600 31413.15161600 -2004.09700782 -17.86212814 78.50640859\n+ 0.00002800 42209.76106550 -481.28911857 -16.02210724 139.74809987\n+ 0.00003000 42689.48379010 2092.57404588 -14.11799868 71.98635054\n+ 0.00003200 32140.35686690 3287.09518295 -12.15586303 -24.51897016\n+ 0.00003400 13442.16919797 1810.83705441 -10.14236807 -39.10004376\n+ 0.00003600 -9231.10226605 -1271.21578790 -8.09221902 20.27669074\n+ 0.00003800 -29408.62646120 -3241.15658461 -6.02052658 45.55495337\n+ 0.00004000 -41627.31520850 -2483.33843193 -3.94447769 -27.79664184\n+ 0.00004200 -42137.13334250 -1.82301038 -1.86595819 -140.52649008\n+ 0.00004400 -30226.42411600 1555.33658588 0.21546106 -185.57828610\n+ 0.00004600 -11806.47895017 960.69346965 2.28847531 -122.35443556\n+ 0.00004800 9446.43397092 -784.52267942 4.34049778 -10.01090329\n+ 0.00005000 24611.29240972 -1447.42762641 6.35945779 66.73347194\n+ 0.00005200 30168.44061035 -598.12158006 8.33652167 81.49338936\n+ 0.00005400 25606.37528575 508.73630130 10.26729402 79.79530240\n+ 0.00005600 13340.52480087 634.81104146 12.15255270 108.71674708\n+ 0.00005800 -585.05665750 -33.15102509 13.99740074 159.07844440\n+ 0.00006000 -9852.88813967 -485.10192035 15.80514484 172.56136499\n+ 0.00006200 -10897.77796887 -375.61072392 17.57305023 116.90827164\n+ 0.00006400 -3757.41661050 -90.31689620 19.29877158 9.99710432\n+ 0.00006600 8790.19739798 242.77363760 20.98538739 -93.21873071\n+ 0.00006800 21442.96733022 1053.59838602 22.64082363 -139.65830590\n+ 0.00007000 28256.12418230 2387.77239428 24.27376738 -102.30945883\n+ 0.00007200 26367.06998670 3253.13344370 25.89205555 -17.58643540\n+ 0.00007400 15591.68871872 2389.26594789 27.50466561 70.86828133\n+ 0.00007600 -1617.68759163 -263.98184134 '..b' 200.58807967 108.17078638 -331.96556974\n+ 0.00012400 15534.72579872 837.18288805 115.44812571 -273.77032314\n+ 0.00012600 15372.19160032 1166.54633476 123.16577183 -143.46280361\n+ 0.00012800 13199.26981327 1270.03948501 131.34284212 84.53268162\n+ 0.00013000 3889.72485947 421.57722256 139.99916669 366.97625240\n+ 0.00013200 -7609.01072867 -804.54137008 149.14109773 588.88717287\n+ 0.00013400 -16485.08328873 -1460.38288014 158.75662442 642.10586107\n+ 0.00013600 -19751.70263360 -1240.39245202 168.82466596 513.59518033\n+ 0.00013800 -14600.56951255 -559.95458905 179.32804534 301.55264267\n+ 0.00014000 -1954.06550150 -51.91954230 190.25821438 121.81791909\n+ 0.00014200 14688.98071130 523.41469312 201.60978325 25.53662766\n+ 0.00014400 28909.92796387 1927.17849885 213.36848057 -16.98627890\n+ 0.00014600 35444.70227900 3986.15244966 225.50204946 -59.14096672\n+ 0.00014800 31753.99162127 5089.68547076 237.96585087 -114.19100870\n+ 0.00015000 19066.65231695 3745.69661691 250.71602572 -172.95897513\n+ 0.00015200 1033.28363425 217.77219521 263.71514409 -202.99390816\n+ 0.00015400 -17523.12332680 -3487.48685363 276.92589903 -176.40811711\n+ 0.00015600 -30732.51592565 -5061.01775777 290.30153120 -85.63379745\n+ 0.00015800 -34893.34868250 -4116.54923544 303.77601724 59.26312152\n+ 0.00016000 -28812.43829975 -2092.85670093 317.27736371 231.49793081\n+ 0.00016200 -15930.13034772 -649.87005150 330.75219166 385.25655146\n+ 0.00016400 -201.63686952 -5.91086837 344.15499751 446.82662611\n+ 0.00016600 2135.67041083 65.54549512 357.42478232 347.74472500\n+ 0.00016800 2769.88369483 94.68015637 370.48840402 101.23584678\n+ 0.00017000 -5563.88881282 -179.12143808 383.27051138 -180.13175856\n+ 0.00017200 -16655.34783006 -272.82554896 395.69587138 -336.42665297\n+ 0.00017400 -25743.73899387 355.10351308 407.69294890 -255.80822779\n+ 0.00017600 -30711.43964525 1657.54592740 419.18969315 47.13427846\n+ 0.00017800 -29741.31364855 2884.74159668 430.11177201 421.77851602\n+ 0.00018000 -22528.97726730 3023.25287064 440.38933481 698.92434815\n+ 0.00018200 -11097.63474715 1754.81618622 449.96430373 797.37749633\n+ 0.00018400 328.48617200 -54.45952336 458.78677146 829.87099890\n+ 0.00018600 5849.23744020 -944.02511479 466.80248629 830.16654232\n+ 0.00018800 3474.25156172 -537.66663608 473.94489081 826.88926756\n+ 0.00019000 -3995.39107607 619.79872886 480.14686318 822.15525974\n+ 0.00019200 -11036.49454635 1830.14069868 485.36230147 831.11133165\n+ 0.00019400 -14001.78241787 2571.36327134 489.57390139 844.75260910\n+ 0.00019600 -12028.77674547 2431.86699351 492.77536795 826.99743344\n+ 0.00019800 -6620.62218248 1426.36740716 494.94559802 744.12013707\n+ 0.00020000 563.32886370 -123.79373740 496.04678396 599.88305724\n' |
| b |
| diff -r 000000000000 -r 4f3222cb5cf6 test-data/NEQGamma_ofrict2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NEQGamma_ofrict2.txt Fri Sep 11 21:54:45 2020 +0000 |
| b |
| b'@@ -0,0 +1,102 @@\n+#x ACF frict_coeff gauss_filtered_frict_coeff av_window_frict_coeff\n+ 0.00000000 820049.57805000 0.00000000 -88.35169831 -280.48699846\n+ 0.00000200 -4358.85795000 -133.28849699 -88.22972067 -88.19151898\n+ 0.00000400 -87816.09622050 -2381.86180009 -87.98019601 206.78227553\n+ 0.00000600 -131399.91872250 -2484.15267240 -87.60563052 420.75577467\n+ 0.00000800 -157962.78872850 -1272.80096612 -87.09850727 415.54857404\n+ 0.00001000 -138547.98040200 423.68679663 -86.46203739 220.05544591\n+ 0.00001200 -75149.24467650 831.83995256 -85.69381797 -19.39421284\n+ 0.00001400 17412.26728800 -230.42745195 -84.78750605 -184.44489621\n+ 0.00001600 115480.21126350 -952.91141368 -83.74024527 -254.60297579\n+ 0.00001800 188259.22998000 590.17608290 -82.55443295 -258.51588475\n+ 0.00002000 212009.57662500 3845.90958964 -81.23547895 -201.73752699\n+ 0.00002200 179721.96976500 5899.47589006 -79.79027794 -63.40787886\n+ 0.00002400 98900.16009300 4279.46998290 -78.22207384 124.26696357\n+ 0.00002600 -2220.79417500 -104.14401258 -76.52588032 336.60454536\n+ 0.00002800 -90011.60591700 -3909.86256270 -74.69455570 356.26981781\n+ 0.00003000 -137133.80762700 -4788.99317502 -72.72531275 198.84495402\n+ 0.00003200 -133164.08762535 -3301.01366740 -70.62158367 8.31697208\n+ 0.00003400 -84350.83000350 -1403.16159163 -68.38850295 -56.74371545\n+ 0.00003600 -5905.70960400 -78.25817913 -66.04439500 18.20705271\n+ 0.00003800 72166.91716950 1135.56715521 -63.58639145 89.69932255\n+ 0.00004000 120505.51429200 2766.59296252 -61.02332288 7.12530570\n+ 0.00004200 114021.51919200 3620.20835160 -58.35161851 -226.91946783\n+ 0.00004400 49243.56428550 1864.88983572 -55.57114618 -478.78785643\n+ 0.00004600 -55557.34158750 -2090.84722338 -52.69410000 -615.02734999\n+ 0.00004800 -147217.76437650 -4421.29824187 -49.73405580 -593.86618618\n+ 0.00005000 -198300.11521500 -3386.87284209 -46.70469036 -455.78564162\n+ 0.00005200 -192130.49563500 -469.37379811 -43.61960647 -279.26540999\n+ 0.00005400 -131119.41096000 1268.58791117 -40.49219486 -129.46297215\n+ 0.00005600 -30325.18489485 476.93398323 -37.33374606 -38.70994611\n+ 0.00005800 75656.48544150 -1061.30425422 -34.15245877 -32.81832328\n+ 0.00006000 146410.57420500 -834.98588086 -30.95661661 -112.68532949\n+ 0.00006200 154533.14829000 862.10811813 -27.76062817 -209.98160347\n+ 0.00006400 102247.69060950 1554.68011169 -24.58254792 -222.45823938\n+ 0.00006600 16240.64970450 319.07926355 -21.43985136 -77.52748335\n+ 0.00006800 -64351.78993350 -1148.25167151 -18.34979444 150.13100453\n+ 0.00007000 -112082.10661935 -1258.58854242 -15.32954316 388.33926875\n+ 0.00007200 -119224.23239265 -304.96491060 -12.39596315 478.34792093\n+ 0.00007400 -82381.22600550 411.89892915 -9.56277546 365.52349202\n+ 0.00007600 -4786.62582450 39.57427761 '..b' 1674.16429547 40.01343067 171.04221469\n+ 0.00012400 19512.94726350 777.13140500 43.14629587 56.04393382\n+ 0.00012600 -36653.09358330 -1436.21101812 46.59846989 -26.86155891\n+ 0.00012800 -32854.20668700 -1201.74753470 50.39600331 -40.13377747\n+ 0.00013000 -21818.38497900 -753.35866591 54.55818681 -7.50287868\n+ 0.00013200 -2973.95105400 -99.92236918 59.09130865 4.44251935\n+ 0.00013400 8564.88182730 289.56830372 63.99700240 -34.78999920\n+ 0.00013600 1934.85723000 66.17677573 69.28874967 -91.56918241\n+ 0.00013800 -24497.09191800 -817.13946083 74.99494252 -123.72241529\n+ 0.00014000 -61646.19561450 -1857.22940676 81.14055026 -132.89858804\n+ 0.00014200 -101891.36043540 -2445.03687958 87.72554000 -155.00683647\n+ 0.00014400 -132974.69188650 -2020.12571316 94.72632160 -212.73380806\n+ 0.00014600 -137663.38560000 -694.65979328 102.11343515 -303.03427244\n+ 0.00014800 -101707.77133650 399.45884033 109.86826252 -358.25769139\n+ 0.00015000 -29564.63915700 261.60803247 117.98170165 -377.49069744\n+ 0.00015200 51251.58621300 -411.84112715 126.43906153 -370.25980842\n+ 0.00015400 113180.97832800 -211.80655002 135.20886135 -370.18806573\n+ 0.00015600 138567.47375250 1048.42865059 144.24815584 -378.03850570\n+ 0.00015800 127159.72719000 2228.83367262 153.50681670 -350.28522288\n+ 0.00016000 82819.23176700 2103.57181338 162.93055802 -236.12084910\n+ 0.00016200 17812.41872085 519.62486357 172.45987082 -39.62300894\n+ 0.00016400 -36119.00680350 -1028.87788255 182.04578703 165.67530387\n+ 0.00016600 -110519.23112100 -2540.67939713 191.65166966 290.61170437\n+ 0.00016800 -106921.60660530 -1586.40765558 201.20240370 307.48058498\n+ 0.00017000 -76446.40564200 -608.74088555 210.62157891 271.62818673\n+ 0.00017200 -23322.73389000 -98.48751533 219.84153297 271.64664462\n+ 0.00017400 29707.45251000 132.55950431 228.81209036 334.73930429\n+ 0.00017600 74300.37906600 621.24243204 237.48578959 407.50929217\n+ 0.00017800 98741.98990950 1466.14801470 245.79589327 425.12644069\n+ 0.00018000 93913.58523300 2072.72739658 253.65590701 373.98926679\n+ 0.00018200 59684.08905900 1660.92937662 260.99073544 290.53799094\n+ 0.00018400 15614.32887000 478.60229674 267.76055483 264.55674776\n+ 0.00018600 -11599.31914500 -357.28218104 273.94457599 316.00064189\n+ 0.00018800 -10596.93693600 -317.58912475 279.50299875 443.03461174\n+ 0.00019000 8761.45959900 261.97719041 284.36758829 522.35499452\n+ 0.00019200 27201.03162900 850.01206613 288.46962428 552.79203880\n+ 0.00019400 36952.05022500 1243.59320758 291.77115090 557.71641457\n+ 0.00019600 38399.36686650 1400.77162096 294.26533754 551.08843935\n+ 0.00019800 30865.52299050 1206.09019462 295.95010795 520.02631775\n+ 0.00020000 10694.24856900 434.54629645 296.80389411 446.71891701\n' |
| b |
| diff -r 000000000000 -r 4f3222cb5cf6 test-data/NEQGamma_outp.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NEQGamma_outp.txt Fri Sep 11 21:54:45 2020 +0000 |
| b |
| b'@@ -0,0 +1,102 @@\n+#x force_integral frict_coeff wdiss corrected_force_integral\n+ 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000\n+ 0.00000200 -0.00392321 -309.80490686 -0.00000031 -0.00392290\n+ 0.00000400 -0.00600385 -1433.31122481 -0.00000205 -0.00600180\n+ 0.00000600 -0.00840497 -1302.42266399 -0.00000479 -0.00840018\n+ 0.00000800 -0.01081599 -696.00283593 -0.00000679 -0.01080921\n+ 0.00001000 -0.01276543 59.67135417 -0.00000742 -0.01275801\n+ 0.00001200 -0.01395301 200.26534006 -0.00000716 -0.01394585\n+ 0.00001400 -0.01428272 -211.00314767 -0.00000717 -0.01427554\n+ 0.00001600 -0.01390386 -299.86397145 -0.00000769 -0.01389617\n+ 0.00001800 -0.01311337 706.27695160 -0.00000728 -0.01310609\n+ 0.00002000 -0.01220919 2436.13821354 -0.00000414 -0.01220505\n+ 0.00002200 -0.01144642 3505.21213240 0.00000181 -0.01144822\n+ 0.00002400 -0.01105948 2809.74173435 0.00000812 -0.01106760\n+ 0.00002600 -0.01123787 993.11451262 0.00001192 -0.01124979\n+ 0.00002800 -0.01205259 -248.07012791 0.00001267 -0.01206525\n+ 0.00003000 -0.01340318 -195.60392001 0.00001222 -0.01341541\n+ 0.00003200 -0.01506203 141.25051892 0.00001217 -0.01507420\n+ 0.00003400 -0.01675665 -363.71528632 0.00001195 -0.01676860\n+ 0.00003600 -0.01826220 -1519.36792976 0.00001006 -0.01827227\n+ 0.00003800 -0.01947399 -1956.43454302 0.00000659 -0.01948058\n+ 0.00004000 -0.02036612 -865.57527338 0.00000377 -0.02036989\n+ 0.00004200 -0.02092478 626.10860652 0.00000353 -0.02092831\n+ 0.00004400 -0.02108110 565.05574074 0.00000472 -0.02108581\n+ 0.00004600 -0.02089789 -1403.86956218 0.00000388 -0.02090177\n+ 0.00004800 -0.02047142 -2830.86397506 -0.00000036 -0.02047107\n+ 0.00005000 -0.01987024 -2293.53919791 -0.00000548 -0.01986476\n+ 0.00005200 -0.01919238 -417.60570188 -0.00000819 -0.01918419\n+ 0.00005400 -0.01839938 834.36904591 -0.00000777 -0.01839160\n+ 0.00005600 -0.01743683 434.72799961 -0.00000650 -0.01743032\n+ 0.00005800 -0.01635230 -519.66723923 -0.00000659 -0.01634571\n+ 0.00006000 -0.01530848 -329.29698187 -0.00000744 -0.01530104\n+ 0.00006200 -0.01449254 858.01810556 -0.00000691 -0.01448563\n+ 0.00006400 -0.01404057 1441.72347492 -0.00000461 -0.01403596\n+ 0.00006600 -0.01404177 879.60901414 -0.00000229 -0.01403949\n+ 0.00006800 -0.01456203 334.25351485 -0.00000108 -0.01456096\n+ 0.00007000 -0.01559948 652.00817770 -0.00000009 -0.01559939\n+ 0.00007200 -0.01700283 1250.72698300 0.00000181 -0.01700464\n+ 0.00007400 -0.01850442 1051.23806218 0.00000412 -0.01850854\n+ 0.00007600 -0.01981895 -253.25084775 0.0000'..b' 2216.16123424 0.00001275 -0.01001629\n+ 0.00012400 -0.01012789 2740.29495857 0.00001771 -0.01014560\n+ 0.00012600 -0.01002803 642.99155129 0.00002109 -0.01004912\n+ 0.00012800 -0.00980763 673.17973142 0.00002241 -0.00983004\n+ 0.00013000 -0.00958833 -276.05014319 0.00002280 -0.00961113\n+ 0.00013200 -0.00971501 -1331.11596207 0.00002120 -0.00973621\n+ 0.00013400 -0.01040330 -2042.60347448 0.00001782 -0.01042112\n+ 0.00013600 -0.01175235 -2339.54888278 0.00001344 -0.01176579\n+ 0.00013800 -0.01367748 -2263.02943488 0.00000884 -0.01368632\n+ 0.00014000 -0.01586775 -1978.10144773 0.00000460 -0.01587234\n+ 0.00014200 -0.01781525 -1395.88433631 0.00000122 -0.01781647\n+ 0.00014400 -0.01894530 -136.33782409 -0.00000031 -0.01894499\n+ 0.00014600 -0.01884929 1692.89613965 0.00000125 -0.01885054\n+ 0.00014800 -0.01750485 2974.81823090 0.00000591 -0.01751076\n+ 0.00015000 -0.01532342 2642.88373319 0.00001153 -0.01533495\n+ 0.00015200 -0.01295535 913.24280375 0.00001509 -0.01297044\n+ 0.00015400 -0.01100340 -927.03460327 0.00001507 -0.01101847\n+ 0.00015600 -0.00985920 -1689.34471443 0.00001246 -0.00987166\n+ 0.00015800 -0.00966688 -1332.07133205 0.00000944 -0.00967631\n+ 0.00016000 -0.01029419 -793.99131765 0.00000731 -0.01030150\n+ 0.00016200 -0.01132573 -941.55813718 0.00000557 -0.01133130\n+ 0.00016400 -0.01208447 -1038.93906805 0.00000359 -0.01208806\n+ 0.00016600 -0.01209668 -2451.04087672 0.00000010 -0.01209679\n+ 0.00016800 -0.01109858 -1619.20548854 -0.00000397 -0.01109462\n+ 0.00017000 -0.00915750 -1037.16157762 -0.00000662 -0.00915087\n+ 0.00017200 -0.00686287 -505.22323695 -0.00000817 -0.00685471\n+ 0.00017400 -0.00489099 169.23053990 -0.00000850 -0.00488249\n+ 0.00017600 -0.00385466 1119.27836540 -0.00000721 -0.00384744\n+ 0.00017800 -0.00413820 2035.34756564 -0.00000406 -0.00413414\n+ 0.00018000 -0.00577393 2281.35445610 0.00000026 -0.00577419\n+ 0.00018200 -0.00843098 1475.48961051 0.00000402 -0.00843500\n+ 0.00018400 -0.01147212 132.45287134 0.00000562 -0.01147774\n+ 0.00018600 -0.01409490 -616.86762340 0.00000514 -0.01410004\n+ 0.00018800 -0.01561112 -391.31151887 0.00000413 -0.01561525\n+ 0.00019000 -0.01567912 413.81613798 0.00000415 -0.01568328\n+ 0.00019200 -0.01440515 1254.39214820 0.00000582 -0.01441097\n+ 0.00019400 -0.01231202 1786.35191510 0.00000886 -0.01232088\n+ 0.00019600 -0.01014927 1765.17722675 0.00001241 -0.01016169\n+ 0.00019800 -0.00865789 1160.67458116 0.00001534 -0.00867323\n+ 0.00020000 -0.00832999 80.82726004 0.00001658 -0.00834657\n' |
| b |
| diff -r 000000000000 -r 4f3222cb5cf6 test-data/NEQGamma_outp1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NEQGamma_outp1.txt Fri Sep 11 21:54:45 2020 +0000 |
| b |
| b'@@ -0,0 +1,102 @@\n+#x force_integral frict_coeff wdiss corrected_force_integral\n+ 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000\n+ 0.00000200 -0.00028893 -1345.26646099 -0.00000135 -0.00028759\n+ 0.00000400 -0.00232537 -1454.28761686 -0.00000414 -0.00232122\n+ 0.00000600 -0.00534240 -264.14035591 -0.00000586 -0.00533654\n+ 0.00000800 -0.00892032 570.71230720 -0.00000556 -0.00891476\n+ 0.00001000 -0.01233174 482.67878751 -0.00000450 -0.01232723\n+ 0.00001200 -0.01484120 -306.50010800 -0.00000433 -0.01483688\n+ 0.00001400 -0.01592271 -678.79838871 -0.00000531 -0.01591740\n+ 0.00001600 -0.01540730 129.24578885 -0.00000586 -0.01540143\n+ 0.00001800 -0.01350838 1433.88087902 -0.00000430 -0.01350408\n+ 0.00002000 -0.01074543 1769.49504443 -0.00000110 -0.01074434\n+ 0.00002200 -0.00782545 525.42519661 0.00000120 -0.00782665\n+ 0.00002400 -0.00551646 -1354.79390711 0.00000037 -0.00551683\n+ 0.00002600 -0.00443259 -2004.09700782 -0.00000299 -0.00442960\n+ 0.00002800 -0.00480792 -481.28911857 -0.00000547 -0.00480244\n+ 0.00003000 -0.00643049 2092.57404588 -0.00000386 -0.00642663\n+ 0.00003200 -0.00878093 3287.09518295 0.00000152 -0.00878245\n+ 0.00003400 -0.01123762 1810.83705441 0.00000661 -0.01124423\n+ 0.00003600 -0.01326588 -1271.21578790 0.00000715 -0.01327304\n+ 0.00003800 -0.01459317 -3241.15658461 0.00000264 -0.01459581\n+ 0.00004000 -0.01524085 -2483.33843193 -0.00000308 -0.01523777\n+ 0.00004200 -0.01546401 -1.82301038 -0.00000557 -0.01545845\n+ 0.00004400 -0.01558410 1555.33658588 -0.00000401 -0.01558009\n+ 0.00004600 -0.01603192 960.69346965 -0.00000150 -0.01603042\n+ 0.00004800 -0.01694582 -784.52267942 -0.00000132 -0.01694450\n+ 0.00005000 -0.01809375 -1447.42762641 -0.00000355 -0.01809019\n+ 0.00005200 -0.01916352 -598.12158006 -0.00000560 -0.01915792\n+ 0.00005400 -0.01967108 508.73630130 -0.00000569 -0.01966539\n+ 0.00005600 -0.01920233 634.81104146 -0.00000455 -0.01919778\n+ 0.00005800 -0.01764643 -33.15102509 -0.00000394 -0.01764248\n+ 0.00006000 -0.01531761 -485.10192035 -0.00000446 -0.01531314\n+ 0.00006200 -0.01285302 -375.61072392 -0.00000532 -0.01284769\n+ 0.00006400 -0.01095150 -90.31689620 -0.00000579 -0.01094571\n+ 0.00006600 -0.01011817 242.77363760 -0.00000564 -0.01011253\n+ 0.00006800 -0.01052398 1053.59838602 -0.00000434 -0.01051964\n+ 0.00007000 -0.01200084 2387.77239428 -0.00000090 -0.01199995\n+ 0.00007200 -0.01412820 3253.13344370 0.00000474 -0.01413295\n+ 0.00007400 -0.01634020 2389.26594789 0.00001038 -0.01635058\n+ 0.00007600 -0.01802042 -263.98184134 0.0000'..b' 200.58807967 -0.00000511 -0.00279048\n+ 0.00012400 -0.00221567 837.18288805 -0.00000407 -0.00221159\n+ 0.00012600 -0.00179223 1166.54633476 -0.00000207 -0.00179016\n+ 0.00012800 -0.00161866 1270.03948501 0.00000037 -0.00161903\n+ 0.00013000 -0.00151181 421.57722256 0.00000206 -0.00151387\n+ 0.00013200 -0.00185055 -804.54137008 0.00000168 -0.00185223\n+ 0.00013400 -0.00284118 -1460.38288014 -0.00000059 -0.00284059\n+ 0.00013600 -0.00463146 -1240.39245202 -0.00000329 -0.00462817\n+ 0.00013800 -0.00718450 -559.95458905 -0.00000509 -0.00717941\n+ 0.00014000 -0.01016260 -51.91954230 -0.00000570 -0.01015689\n+ 0.00014200 -0.01298551 523.41469312 -0.00000523 -0.01298028\n+ 0.00014400 -0.01501735 1927.17849885 -0.00000278 -0.01501457\n+ 0.00014600 -0.01576224 3986.15244966 0.00000313 -0.01576537\n+ 0.00014800 -0.01501718 5089.68547076 0.00001221 -0.01502939\n+ 0.00015000 -0.01296828 3745.69661691 0.00002104 -0.01298932\n+ 0.00015200 -0.01017811 217.77219521 0.00002501 -0.01020312\n+ 0.00015400 -0.00739771 -3487.48685363 0.00002174 -0.00741945\n+ 0.00015600 -0.00530829 -5061.01775777 0.00001319 -0.00532148\n+ 0.00015800 -0.00432459 -4116.54923544 0.00000401 -0.00432860\n+ 0.00016000 -0.00449294 -2092.85670093 -0.00000220 -0.00449074\n+ 0.00016200 -0.00550412 -649.87005150 -0.00000494 -0.00549918\n+ 0.00016400 -0.00660743 -5.91086837 -0.00000560 -0.00660183\n+ 0.00016600 -0.00753781 65.54549512 -0.00000554 -0.00753227\n+ 0.00016800 -0.00787258 94.68015637 -0.00000538 -0.00786720\n+ 0.00017000 -0.00715284 -179.12143808 -0.00000546 -0.00714738\n+ 0.00017200 -0.00581344 -272.82554896 -0.00000591 -0.00580753\n+ 0.00017400 -0.00439586 355.10351308 -0.00000583 -0.00439003\n+ 0.00017600 -0.00348190 1657.54592740 -0.00000382 -0.00347808\n+ 0.00017800 -0.00349891 2884.74159668 0.00000072 -0.00349964\n+ 0.00018000 -0.00462675 3023.25287064 0.00000663 -0.00463339\n+ 0.00018200 -0.00676588 1754.81618622 0.00001141 -0.00677729\n+ 0.00018400 -0.00947283 -54.45952336 0.00001311 -0.00948594\n+ 0.00018600 -0.01198297 -944.02511479 0.00001211 -0.01199508\n+ 0.00018800 -0.01351134 -537.66663608 0.00001063 -0.01352197\n+ 0.00019000 -0.01359850 619.79872886 0.00001071 -0.01360921\n+ 0.00019200 -0.01230380 1830.14069868 0.00001316 -0.01231696\n+ 0.00019400 -0.01014874 2571.36327134 0.00001756 -0.01016630\n+ 0.00019600 -0.00786581 2431.86699351 0.00002257 -0.00788837\n+ 0.00019800 -0.00618981 1426.36740716 0.00002643 -0.00621624\n+ 0.00020000 -0.00567906 -123.79373740 0.00002773 -0.00570679\n' |
| b |
| diff -r 000000000000 -r 4f3222cb5cf6 test-data/NEQGamma_outp2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NEQGamma_outp2.txt Fri Sep 11 21:54:45 2020 +0000 |
| b |
| b'@@ -0,0 +1,102 @@\n+#x force_integral frict_coeff wdiss corrected_force_integral\n+ 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000\n+ 0.00000200 -0.00330406 -133.28849699 -0.00000013 -0.00330393\n+ 0.00000400 -0.00636445 -2381.86180009 -0.00000265 -0.00636180\n+ 0.00000600 -0.00965354 -2484.15267240 -0.00000751 -0.00964603\n+ 0.00000800 -0.01252890 -1272.80096612 -0.00001127 -0.01251763\n+ 0.00001000 -0.01442164 423.68679663 -0.00001212 -0.01440951\n+ 0.00001200 -0.01503189 831.83995256 -0.00001086 -0.01502103\n+ 0.00001400 -0.01441631 -230.42745195 -0.00001026 -0.01440604\n+ 0.00001600 -0.01302548 -952.91141368 -0.00001145 -0.01301403\n+ 0.00001800 -0.01151471 590.17608290 -0.00001181 -0.01150290\n+ 0.00002000 -0.01045748 3845.90958964 -0.00000737 -0.01045010\n+ 0.00002200 -0.01022110 5899.47589006 0.00000237 -0.01022347\n+ 0.00002400 -0.01098400 4279.46998290 0.00001255 -0.01099655\n+ 0.00002600 -0.01275202 -104.14401258 0.00001673 -0.01276875\n+ 0.00002800 -0.01533740 -3909.86256270 0.00001271 -0.01535011\n+ 0.00003000 -0.01834052 -4788.99317502 0.00000401 -0.01834454\n+ 0.00003200 -0.02122997 -3301.01366740 -0.00000408 -0.02122589\n+ 0.00003400 -0.02350381 -1403.16159163 -0.00000878 -0.02349503\n+ 0.00003600 -0.02483672 -78.25817913 -0.00001026 -0.02482646\n+ 0.00003800 -0.02517675 1135.56715521 -0.00000921 -0.02516755\n+ 0.00004000 -0.02469464 2766.59296252 -0.00000530 -0.02468934\n+ 0.00004200 -0.02365645 3620.20835160 0.00000108 -0.02365753\n+ 0.00004400 -0.02230644 1864.88983572 0.00000657 -0.02231301\n+ 0.00004600 -0.02092224 -2090.84722338 0.00000634 -0.02092858\n+ 0.00004800 -0.01977588 -4421.29824187 -0.00000017 -0.01977571\n+ 0.00005000 -0.01901760 -3386.87284209 -0.00000798 -0.01900962\n+ 0.00005200 -0.01861994 -469.37379811 -0.00001183 -0.01860811\n+ 0.00005400 -0.01835163 1268.58791117 -0.00001103 -0.01834059\n+ 0.00005600 -0.01796265 476.93398323 -0.00000929 -0.01795336\n+ 0.00005800 -0.01738252 -1061.30425422 -0.00000987 -0.01737265\n+ 0.00006000 -0.01676130 -834.98588086 -0.00001177 -0.01674953\n+ 0.00006200 -0.01633255 862.10811813 -0.00001174 -0.01632081\n+ 0.00006400 -0.01629663 1554.68011169 -0.00000933 -0.01628730\n+ 0.00006600 -0.01682112 319.07926355 -0.00000745 -0.01681367\n+ 0.00006800 -0.01803550 -1148.25167151 -0.00000828 -0.01802722\n+ 0.00007000 -0.01990021 -1258.58854242 -0.00001069 -0.01988953\n+ 0.00007200 -0.02209227 -304.96491060 -0.00001225 -0.02208002\n+ 0.00007400 -0.02412258 411.89892915 -0.00001214 -0.02411044\n+ 0.00007600 -0.02554865 39.57427761 -0.0000'..b' 1674.16429547 0.00000611 -0.01477377\n+ 0.00012400 -0.01567924 777.13140500 0.00000856 -0.01568779\n+ 0.00012600 -0.01639225 -1436.21101812 0.00000790 -0.01640015\n+ 0.00012800 -0.01675034 -1201.74753470 0.00000526 -0.01675560\n+ 0.00013000 -0.01683481 -753.35866591 0.00000331 -0.01683811\n+ 0.00013200 -0.01677711 -99.92236918 0.00000245 -0.01677956\n+ 0.00013400 -0.01680665 289.56830372 0.00000264 -0.01680929\n+ 0.00013600 -0.01717171 66.17677573 0.00000300 -0.01717471\n+ 0.00013800 -0.01805922 -817.13946083 0.00000225 -0.01806146\n+ 0.00014000 -0.01950682 -1857.22940676 -0.00000043 -0.01950640\n+ 0.00014200 -0.02128489 -2445.03687958 -0.00000473 -0.02128016\n+ 0.00014400 -0.02288252 -2020.12571316 -0.00000920 -0.02287333\n+ 0.00014600 -0.02372178 -694.65979328 -0.00001191 -0.02370987\n+ 0.00014800 -0.02349327 399.45884033 -0.00001221 -0.02348107\n+ 0.00015000 -0.02231618 261.60803247 -0.00001154 -0.02230464\n+ 0.00015200 -0.02058259 -411.84112715 -0.00001169 -0.02057090\n+ 0.00015400 -0.01869749 -211.80655002 -0.00001232 -0.01868517\n+ 0.00015600 -0.01700933 1048.42865059 -0.00001148 -0.01699785\n+ 0.00015800 -0.01583020 2228.83367262 -0.00000820 -0.01582200\n+ 0.00016000 -0.01534495 2103.57181338 -0.00000387 -0.01534108\n+ 0.00016200 -0.01544411 519.62486357 -0.00000125 -0.01544286\n+ 0.00016400 -0.01569072 -1028.87788255 -0.00000176 -0.01568896\n+ 0.00016600 -0.01528460 -2540.67939713 -0.00000533 -0.01527927\n+ 0.00016800 -0.01372341 -1586.40765558 -0.00000945 -0.01371395\n+ 0.00017000 -0.01111279 -608.74088555 -0.00001165 -0.01110114\n+ 0.00017200 -0.00787247 -98.48751533 -0.00001236 -0.00786012\n+ 0.00017400 -0.00473024 132.55950431 -0.00001232 -0.00471792\n+ 0.00017600 -0.00244342 621.24243204 -0.00001157 -0.00243186\n+ 0.00017800 -0.00158672 1466.14801470 -0.00000948 -0.00157723\n+ 0.00018000 -0.00237524 2072.72739658 -0.00000594 -0.00236930\n+ 0.00018200 -0.00458287 1660.92937662 -0.00000221 -0.00458066\n+ 0.00018400 -0.00756423 478.60229674 -0.00000007 -0.00756416\n+ 0.00018600 -0.01037347 -357.28218104 0.00000005 -0.01037352\n+ 0.00018800 -0.01208003 -317.58912475 -0.00000062 -0.01207941\n+ 0.00019000 -0.01212748 261.97719041 -0.00000068 -0.01212680\n+ 0.00019200 -0.01054721 850.01206613 0.00000043 -0.01054764\n+ 0.00019400 -0.00795757 1243.59320758 0.00000253 -0.00796010\n+ 0.00019600 -0.00530655 1400.77162096 0.00000517 -0.00531172\n+ 0.00019800 -0.00351460 1206.09019462 0.00000778 -0.00352238\n+ 0.00020000 -0.00315052 434.54629645 0.00000942 -0.00315994\n' |
| b |
| diff -r 000000000000 -r 4f3222cb5cf6 test-data/Z.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Z.tabular Fri Sep 11 21:54:45 2020 +0000 |
| b |
| @@ -0,0 +1,3 @@ +0.000000000000000000e+00 3.000000000000000000e+00 1.518774317977597654e+00 2.000000000000000000e+00 +1.000000000000000000e+00 4.000000000000000000e+00 1.667784261923495492e+00 3.000000000000000000e+00 +2.000000000000000000e+00 5.000000000000000000e+00 2.332608798402487249e+00 4.000000000000000000e+00 |
| b |
| diff -r 000000000000 -r 4f3222cb5cf6 test-data/clusters.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clusters.json Fri Sep 11 21:54:45 2020 +0000 |
| [ |
| @@ -0,0 +1,7 @@ +{ + "1": [ + 0, + 1, + 3 + ] +} \ No newline at end of file |
| b |
| diff -r 000000000000 -r 4f3222cb5cf6 test-data/contacts.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/contacts.dat Fri Sep 11 21:54:45 2020 +0000 |
| b |
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| b |
| diff -r 000000000000 -r 4f3222cb5cf6 test-data/contacts2.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/contacts2.dat Fri Sep 11 21:54:45 2020 +0000 |
| b |
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| b |
| diff -r 000000000000 -r 4f3222cb5cf6 test-data/cov.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cov.dat Fri Sep 11 21:54:45 2020 +0000 |
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| b |
| diff -r 000000000000 -r 4f3222cb5cf6 test-data/dendrogram.png |
| b |
| Binary file test-data/dendrogram.png has changed |
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| diff -r 000000000000 -r 4f3222cb5cf6 test-data/heatmap.png |
| b |
| Binary file test-data/heatmap.png has changed |
| b |
| diff -r 000000000000 -r 4f3222cb5cf6 test-data/inp.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inp.json Fri Sep 11 21:54:45 2020 +0000 |
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| diff -r 000000000000 -r 4f3222cb5cf6 test-data/outp.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outp.txt Fri Sep 11 21:54:45 2020 +0000 |
| b |
| @@ -0,0 +1,16 @@ +Frame resid_212_and_name_OE2-resid_3_and_name_C1 +0 3.893687 +1 3.783451 +2 3.766245 +3 3.780305 +4 3.635230 +5 3.649891 +6 3.694009 +7 3.734515 +8 3.710876 +9 3.693928 +10 3.724796 +11 3.426413 +12 3.389410 +13 3.344683 +14 3.262913 |
| b |
| diff -r 000000000000 -r 4f3222cb5cf6 test-data/outp_mat.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outp_mat.tabular Fri Sep 11 21:54:45 2020 +0000 |
| b |
| @@ -0,0 +1,4 @@ +0.000000000000000000e+00 1.088254137623131168e+00 1.258145647545655832e+00 1.001874561823538956e+00 +1.088254137623131168e+00 0.000000000000000000e+00 1.642391617355136280e+00 1.220435985614184204e+00 +1.258145647545655832e+00 1.642391617355136280e+00 0.000000000000000000e+00 1.788898050038353560e+00 +1.001874561823538956e+00 1.220435985614184204e+00 1.788898050038353560e+00 0.000000000000000000e+00 |
| b |
| diff -r 000000000000 -r 4f3222cb5cf6 test-data/output.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.json Fri Sep 11 21:54:45 2020 +0000 |
| [ |
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| b |
| diff -r 000000000000 -r 4f3222cb5cf6 test-data/proj2.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/proj2.dat Fri Sep 11 21:54:45 2020 +0000 |
| b |
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| b |
| diff -r 000000000000 -r 4f3222cb5cf6 test-data/pull1.xvg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pull1.xvg Fri Sep 11 21:54:45 2020 +0000 |
| b |
| @@ -0,0 +1,118 @@ +# This file was created Sat Jan 11 15:16:55 2020 +# Created by: +# :-) GROMACS - gmx mdrun, 2019.1 (-: +# +# Executable: /usr/local/bin/gmx +# Data prefix: /usr/local +# Working dir: /data/share/staging/6673623/working +# Command line: +# gmx mdrun -nt 16 -deffnm outp +# gmx mdrun is part of G R O M A C S: +# +# God Rules Over Mankind, Animals, Cosmos and Such +# +@ title "Pull force" +@ xaxis label "Time (ps)" +@ yaxis label "Force (kJ/mol/nm)" +@TYPE xy +0.0000 6024.09 +0.0020 -1440.45 +0.0040 -2511.27 +0.0060 -2897.63 +0.0080 -2775.86 +0.0100 -1984.12 +0.0120 -692.582 +0.0140 749.852 +0.0160 1926.04 +0.0180 2521.88 +0.0200 2405.94 +0.0220 1618.47 +0.0240 312.892 +0.0260 -1146.03 +0.0280 -2331.23 +0.0300 -2868.38 +0.0320 -2634.84 +0.0340 -1742.36 +0.0360 -463.328 +0.0380 764.038 +0.0400 1581.21 +0.0420 1724.85 +0.0440 1203.93 +0.0460 119.215 +0.0480 -933.681 +0.0500 -1649.19 +0.0520 -1728.6 +0.0540 -1128.9 +0.0560 -43.2839 +0.0580 1061.76 +0.0600 1706.84 +0.0620 1632.03 +0.0640 886.953 +0.0660 -265.667 +0.0680 -1413.95 +0.0700 -2156.87 +0.0720 -2271.91 +0.0740 -1707.92 +0.0760 -561.06 +0.0780 847.304 +0.0800 1993.62 +0.0820 2439.33 +0.0840 2183.08 +0.0860 1162.58 +0.0880 245.372 +0.0900 -674.664 +0.0920 -1389.64 +0.0940 -1732.39 +0.0960 -1659.95 +0.0980 -1215.14 +0.1000 -560.687 +0.1020 56.7457 +0.1040 541.266 +0.1060 941.849 +0.1080 1290.27 +0.1100 1550.28 +0.1120 1620.82 +0.1140 1483.18 +0.1160 1200.91 +0.1180 835.327 +0.1200 414.748 +0.1220 -21.986 +0.1240 -268.239 +0.1260 -610.519 +0.1280 -419.701 +0.1300 -193.452 +0.1320 11.4089 +0.1340 13.1112 +0.1360 -276.636 +0.1380 -829.048 +0.1400 -1451.56 +0.1420 -1907.91 +0.1440 -1960.87 +0.1460 -1495.45 +0.1480 -590.751 +0.1500 498.442 +0.1520 1444.86 +0.1540 2030.3 +0.1560 2092.26 +0.1580 1656.44 +0.1600 859.3 +0.1620 14.6479 +0.1640 -438.284 +0.1660 -573.584 +0.1680 32.1338 +0.1700 805.322 +0.1720 1470.23 +0.1740 1733.74 +0.1760 1558.83 +0.1780 971.192 +0.1800 103.252 +0.1820 -825.594 +0.1840 -1427.63 +0.1860 -1342.79 +0.1880 -578.404 +0.1900 513.202 +0.1920 1414.83 +0.1940 1795.16 +0.1960 1584.51 +0.1980 877.231 +0.2000 -111.269 |
| b |
| diff -r 000000000000 -r 4f3222cb5cf6 test-data/pull2.xvg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pull2.xvg Fri Sep 11 21:54:45 2020 +0000 |
| b |
| @@ -0,0 +1,118 @@ +# This file was created Sat Jan 11 15:14:02 2020 +# Created by: +# :-) GROMACS - gmx mdrun, 2019.1 (-: +# +# Executable: /usr/local/bin/gmx +# Data prefix: /usr/local +# Working dir: /data/share/staging/6673627/working +# Command line: +# gmx mdrun -nt 16 -deffnm outp +# gmx mdrun is part of G R O M A C S: +# +# GROup of MAchos and Cynical Suckers +# +@ title "Pull force" +@ xaxis label "Time (ps)" +@ yaxis label "Force (kJ/mol/nm)" +@TYPE xy +0.0000 -5098.38 +0.0020 -63.1292 +0.0040 -58.0201 +0.0060 -567.151 +0.0080 -915.192 +0.0100 -1147.66 +0.0120 -1194.57 +0.0140 -1025.71 +0.0160 -619.358 +0.0180 -30.7206 +0.0200 628.788 +0.0220 1186.76 +0.0240 1499.87 +0.0260 1501.01 +0.0280 1225.59 +0.0300 728.864 +0.0320 73.4782 +0.0340 -609.651 +0.0360 -1241.19 +0.0380 -1714.09 +0.0400 -1926.53 +0.0420 -1825.85 +0.0440 -1343.11 +0.0460 -875.662 +0.0480 -137.674 +0.0500 424.689 +0.0520 813.554 +0.0540 1028.83 +0.0560 1080.86 +0.0580 1012.46 +0.0600 876.583 +0.0620 713.725 +0.0640 570.333 +0.0660 475.042 +0.0680 392.949 +0.0700 224.142 +0.0720 -50.0798 +0.0740 -394.081 +0.0760 -697.375 +0.0780 -847.788 +0.0800 -757.177 +0.0820 -440.838 +0.0840 160.155 +0.0860 304.292 +0.0880 804.365 +0.0900 951.843 +0.0920 801.215 +0.0940 418.322 +0.0960 -64.6304 +0.0980 -449.703 +0.1000 -559.593 +0.1020 -338.869 +0.1040 98.9362 +0.1060 546.434 +0.1080 882.254 +0.1100 1007.2 +0.1120 882.558 +0.1140 546.07 +0.1160 148.665 +0.1180 -57.5016 +0.1200 49.9737 +0.1220 409.28 +0.1240 1040.8 +0.1260 684.824 +0.1280 692.54 +0.1300 134.317 +0.1320 -629.767 +0.1340 -1376.01 +0.1360 -1941.02 +0.1380 -2059.37 +0.1400 -1616.22 +0.1420 -670.138 +0.1440 475.235 +0.1460 1491.31 +0.1480 2085.01 +0.1500 2105.1 +0.1520 1531.93 +0.1540 553.708 +0.1560 -497.426 +0.1580 -1283.86 +0.1600 -1568.59 +0.1620 -1327.71 +0.1640 -455.275 +0.1660 -393.621 +0.1680 265.539 +0.1700 336.479 +0.1720 66.7614 +0.1740 -435.565 +0.1760 -1029.08 +0.1780 -1534.97 +0.1800 -1795.16 +0.1820 -1760.74 +0.1840 -1399.95 +0.1860 -849.902 +0.1880 -285.645 +0.1900 176.529 +0.1920 484.836 +0.1940 615.295 +0.1960 570.901 +0.1980 319.342 +0.2000 -63.7999 |
| b |
| diff -r 000000000000 -r 4f3222cb5cf6 test-data/pull3.xvg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pull3.xvg Fri Sep 11 21:54:45 2020 +0000 |
| b |
| @@ -0,0 +1,118 @@ +# This file was created Sat Jan 11 11:17:19 2020 +# Created by: +# :-) GROMACS - gmx mdrun, 2019.1 (-: +# +# Executable: /usr/local/bin/gmx +# Data prefix: /usr/local +# Working dir: /data/share/staging/6671882/working +# Command line: +# gmx mdrun -nt 16 -deffnm outp +# gmx mdrun is part of G R O M A C S: +# +# Gyas ROwers Mature At Cryogenic Speed +# +@ title "Pull force" +@ xaxis label "Time (ps)" +@ yaxis label "Force (kJ/mol/nm)" +@TYPE xy +0.0000 -9835.61 +0.0020 -1356.15 +0.0040 -812.913 +0.0060 -356.365 +0.0080 279.129 +0.0100 695.388 +0.0120 760.799 +0.0140 413.1 +0.0160 -307.339 +0.0180 -1119.04 +0.0200 -1694.31 +0.0220 -1857.34 +0.0240 -1599.83 +0.0260 -1103.08 +0.0280 -590.412 +0.0300 -216.222 +0.0320 -59.4561 +0.0340 -111.021 +0.0360 -349.112 +0.0380 -631.665 +0.0400 -749.358 +0.0420 -480.318 +0.0440 251.563 +0.0460 1193.69 +0.0480 1913.5 +0.0500 2185.92 +0.0520 1987.19 +0.0540 1406.94 +0.0560 543.203 +0.0580 -401.431 +0.0600 -1124.73 +0.0620 -1356.63 +0.0640 -1090.51 +0.0660 -579.76 +0.0680 -169.391 +0.0700 10.7899 +0.0720 33.8781 +0.0740 -114.673 +0.0760 -468.487 +0.0780 -956.942 +0.0800 -1266.95 +0.0820 -1152.33 +0.0840 -799.059 +0.0860 -57.2971 +0.0880 86.3943 +0.0900 82.0647 +0.0920 63.9564 +0.0940 41.5732 +0.0960 -114.408 +0.0980 -342.996 +0.1000 -289.586 +0.1020 234.269 +0.1040 1023.25 +0.1060 1617.73 +0.1080 1778.66 +0.1100 1502.41 +0.1120 939.611 +0.1140 235.798 +0.1160 -441.056 +0.1180 -924.133 +0.1200 -1084.76 +0.1220 -887.306 +0.1240 -645.618 +0.1260 98.3492 +0.1280 215.697 +0.1300 228.514 +0.1320 68.9249 +0.1340 -152.533 +0.1360 -314.056 +0.1380 -355.276 +0.1400 -259.327 +0.1420 62.6616 +0.1440 610.851 +0.1460 1166.95 +0.1480 1376.27 +0.1500 1070.22 +0.1520 453.658 +0.1540 -158.612 +0.1560 -587.625 +0.1580 -802.82 +0.1600 -742.418 +0.1620 -329.843 +0.1640 260.255 +0.1660 1563.85 +0.1680 2099.99 +0.1700 2283.79 +0.1720 1921.29 +0.1740 1159.2 +0.1760 121.866 +0.1780 -938.471 +0.1800 -1713.03 +0.1820 -1979.88 +0.1840 -1729.61 +0.1860 -1118.46 +0.1880 -373.46 +0.1900 343.756 +0.1920 888.764 +0.1940 1080.51 +0.1960 841.869 +0.1980 280.294 +0.2000 -318.095 |
| b |
| diff -r 000000000000 -r 4f3222cb5cf6 test-data/stats.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stats.dat Fri Sep 11 21:54:45 2020 +0000 |
| b |
| @@ -0,0 +1,85 @@ + 1.967497e+01 3.703805e-01 + 1.945682e+01 4.155976e-01 + 2.493662e+01 4.482403e-01 + 2.591100e+01 4.907198e-01 + 2.054311e+01 6.191418e-01 + 2.042238e+01 8.120932e-01 + 2.045441e+01 1.071626e+00 + 2.357741e+01 8.641369e-01 + 2.260843e+01 5.896767e-01 + 1.992950e+01 5.709322e-01 + 2.399211e+01 6.546606e-01 + 7.845941e+00 6.782487e-01 + 1.052719e+01 5.837915e-01 + 1.169832e+01 5.493730e-01 + 9.145760e+00 4.060450e-01 + 6.055308e+00 5.063536e-01 + 8.693517e+00 5.978220e-01 + 6.830967e+00 4.033432e-01 + 6.361173e+00 5.483321e-01 + 9.094970e+00 3.961013e-01 + 1.174759e+01 2.980387e-01 + 8.827140e+00 3.946120e-01 + 7.463399e+00 1.994348e-01 + 7.811651e+00 3.917859e-01 + 4.275341e+00 3.092223e-01 + 6.986056e+00 3.965528e-01 + 9.001224e+00 3.904505e-01 + 7.288267e+00 4.367149e-01 + 7.595355e+00 4.232301e-01 + 1.187438e+01 4.095508e-01 + 1.120698e+01 3.917284e-01 + 1.026656e+01 4.369231e-01 + 8.465002e+00 4.423827e-01 + 1.063072e+01 3.827076e-01 + 9.867346e+00 2.945949e-01 + 6.202634e+00 3.185203e-01 + 7.599270e+00 3.198939e-01 + 1.015873e+01 2.974711e-01 + 8.666472e+00 4.832279e-01 + 9.860568e+00 4.691489e-01 + 1.159276e+01 4.520981e-01 + 9.175733e+00 6.050901e-01 + 6.679121e+00 4.572131e-01 + 1.011808e+01 4.204646e-01 + 1.109328e+01 5.258842e-01 + 8.433053e+00 5.673694e-01 + 9.695981e+00 4.866417e-01 + 1.313777e+01 5.016506e-01 + 1.302361e+01 6.386153e-01 + 1.409427e+01 6.219133e-01 + 1.320250e+01 6.857931e-01 + 1.588558e+01 6.652152e-01 + 1.526147e+01 6.511772e-01 + 1.155960e+01 6.547106e-01 + 1.324390e+01 6.993882e-01 + 1.565683e+01 6.830393e-01 + 1.345531e+01 6.707395e-01 + 1.114576e+01 6.897825e-01 + 1.465040e+01 7.207709e-01 + 1.589369e+01 6.305320e-01 + 1.441524e+01 5.350904e-01 + 1.610456e+01 4.926006e-01 + 1.371388e+01 5.174074e-01 + 1.519495e+01 5.841832e-01 + 1.861954e+01 5.504953e-01 + 1.862698e+01 5.103952e-01 + 1.729435e+01 5.644140e-01 + 1.788582e+01 6.753580e-01 + 1.864438e+01 6.108037e-01 + 1.552720e+01 5.975017e-01 + 1.336845e+01 6.492108e-01 + 1.557286e+01 6.782724e-01 + 1.501091e+01 6.114845e-01 + 1.116047e+01 6.095425e-01 + 1.159290e+01 6.456012e-01 + 1.440479e+01 6.038611e-01 + 1.025204e+01 5.762923e-01 + 1.380680e+01 6.147225e-01 + 1.578026e+01 5.726969e-01 + 1.392271e+01 5.035768e-01 + 1.653598e+01 4.746090e-01 + 1.721792e+01 4.686125e-01 + 1.960588e+01 5.201088e-01 + 1.831822e+01 5.600042e-01 + 2.224398e+01 5.684325e-01 |
| b |
| diff -r 000000000000 -r 4f3222cb5cf6 test-data/traj_cut.dcd |
| b |
| Binary file test-data/traj_cut.dcd has changed |
| b |
| diff -r 000000000000 -r 4f3222cb5cf6 test-data/val.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/val.dat Fri Sep 11 21:54:45 2020 +0000 |
| b |
| @@ -0,0 +1,85 @@ + 3.947222e+01 + 2.015408e+01 + 4.916455e+00 + 2.895004e+00 + 2.441851e+00 + 1.693793e+00 + 1.452903e+00 + 1.162406e+00 + 9.084163e-01 + 8.297056e-01 + 7.989324e-01 + 6.787932e-01 + 5.389385e-01 + 4.860497e-01 + 4.819947e-01 + 4.578189e-01 + 4.253657e-01 + 3.982626e-01 + 3.460761e-01 + 3.256565e-01 + 2.848984e-01 + 2.736597e-01 + 2.479534e-01 + 2.340745e-01 + 2.225551e-01 + 1.889215e-01 + 1.785513e-01 + 1.644114e-01 + 1.600505e-01 + 1.454533e-01 + 1.354044e-01 + 1.321860e-01 + 1.232544e-01 + 1.200232e-01 + 1.047262e-01 + 9.791054e-02 + 9.288343e-02 + 8.730712e-02 + 8.455886e-02 + 7.553146e-02 + 7.464053e-02 + 6.972549e-02 + 6.652490e-02 + 6.060531e-02 + 5.676623e-02 + 5.018758e-02 + 4.989483e-02 + 4.465919e-02 + 4.245154e-02 + 4.105765e-02 + 3.892739e-02 + 3.643910e-02 + 3.230759e-02 + 3.081278e-02 + 2.805245e-02 + 2.607806e-02 + 2.512062e-02 + 2.207873e-02 + 2.048675e-02 + 1.852247e-02 + 1.676865e-02 + 1.442674e-02 + 1.345403e-02 + 1.305317e-02 + 1.238466e-02 + 1.052215e-02 + 1.002042e-02 + 8.120974e-03 + 6.890932e-03 + 6.279938e-03 + 5.707040e-03 + 5.157449e-03 + 4.203168e-03 + 3.501119e-03 + 2.816421e-03 + 2.464797e-03 + 2.086617e-03 + 1.873654e-03 + 1.403892e-03 + 1.196570e-03 + 1.101350e-03 + 8.899093e-04 + 7.096377e-04 + 3.600828e-04 + 2.338050e-04 |
| b |
| diff -r 000000000000 -r 4f3222cb5cf6 test-data/val2.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/val2.dat Fri Sep 11 21:54:45 2020 +0000 |
| b |
| @@ -0,0 +1,85 @@ + 3.947222e+01 + 2.015408e+01 + 4.916455e+00 + 2.895004e+00 + 2.441851e+00 + 1.693793e+00 + 1.452903e+00 + 1.162406e+00 + 9.084164e-01 + 8.297056e-01 + 7.989324e-01 + 6.787932e-01 + 5.389385e-01 + 4.860497e-01 + 4.819947e-01 + 4.578189e-01 + 4.253657e-01 + 3.982626e-01 + 3.460761e-01 + 3.256565e-01 + 2.848984e-01 + 2.736597e-01 + 2.479534e-01 + 2.340746e-01 + 2.225550e-01 + 1.889216e-01 + 1.785514e-01 + 1.644114e-01 + 1.600505e-01 + 1.454532e-01 + 1.354044e-01 + 1.321860e-01 + 1.232545e-01 + 1.200232e-01 + 1.047262e-01 + 9.791049e-02 + 9.288340e-02 + 8.730713e-02 + 8.455885e-02 + 7.553143e-02 + 7.464052e-02 + 6.972550e-02 + 6.652490e-02 + 6.060527e-02 + 5.676623e-02 + 5.018758e-02 + 4.989473e-02 + 4.465916e-02 + 4.245147e-02 + 4.105768e-02 + 3.892737e-02 + 3.643909e-02 + 3.230761e-02 + 3.081277e-02 + 2.805252e-02 + 2.607810e-02 + 2.512066e-02 + 2.207874e-02 + 2.048678e-02 + 1.852242e-02 + 1.676865e-02 + 1.442676e-02 + 1.345409e-02 + 1.305316e-02 + 1.238469e-02 + 1.052216e-02 + 1.002041e-02 + 8.120949e-03 + 6.890981e-03 + 6.280023e-03 + 5.707032e-03 + 5.157477e-03 + 4.203180e-03 + 3.501140e-03 + 2.816480e-03 + 2.464769e-03 + 2.086600e-03 + 1.873642e-03 + 1.403898e-03 + 1.196546e-03 + 1.101421e-03 + 8.898859e-04 + 7.096480e-04 + 3.601291e-04 + 2.338039e-04 |
| b |
| diff -r 000000000000 -r 4f3222cb5cf6 test-data/vec.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vec.dat Fri Sep 11 21:54:45 2020 +0000 |
| b |
| b'@@ -0,0 +1,85 @@\n+ 3.597432e-02 2.692211e-02 2.817930e-01 8.201814e-02 -4.862062e-02 4.934469e-02 -5.074872e-03 -2.150250e-01 -1.988593e-01 -1.338510e-01 4.586823e-01 -8.329182e-03 -5.065555e-01 3.370271e-01 1.334040e-01 1.022590e-01 -1.449047e-01 1.035877e-01 1.174587e-01 9.936859e-02 -1.399434e-03 2.743653e-02 -1.961464e-02 6.141477e-02 7.851144e-03 3.421684e-02 -1.351951e-01 4.919332e-02 2.986516e-03 1.657092e-01 3.669791e-02 2.844914e-02 1.034812e-01 5.922159e-02 5.962049e-06 3.234775e-02 4.998555e-02 1.455689e-02 -3.058247e-02 1.714270e-02 3.528911e-02 8.575856e-02 -1.485020e-02 -4.939949e-02 5.514172e-02 5.081083e-02 8.656934e-03 -7.573655e-03 -8.480181e-02 3.290604e-02 -5.798370e-02 8.662148e-02 1.820673e-02 -2.277328e-03 -6.032412e-02 1.971969e-02 -3.662553e-02 3.839312e-02 -1.826046e-02 -2.437585e-02 -5.313370e-02 4.283162e-02 4.242042e-02 5.622661e-02 -2.380492e-02 -1.038485e-02 1.298166e-03 2.784345e-02 1.000499e-02 2.916464e-02 -3.485203e-03 -4.176440e-03 -1.341336e-02 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