repopulate MDANSE

7b7e1694 · eric pellegrini · 5a2bf9e8 · 7b7e1694 · 7b7e1694 · 7b7e1694
Commit 7b7e1694 authored Mar 26, 2015 by eric pellegrini
13 changed files
--- a/Data/Trajectories/DL_Poly/FIELD_Water
+++ b/Data/Trajectories/DL_Poly/FIELD_Water
+SPCE box
+units kJ
+molecular types 1
+spce water
+nummols  256
+atoms 3
+OW        16.0000      -0.82000     1    0    0d.a
+HW         1.0000       0.41000     1    0    0.h.
+HW         1.0000       0.41000     1    0    0.h.
+constraints 3
+   1    2    1.000
+   1    3    1.000
+   2    3    1.633
+finish
+vdW 3
+   OW      OW   12-6 0.26330E+07      2617.0 1.0000 1.0000 1.0000
+   OW      HW   12-6 0.00000E+00 0.00000E+00 1.0000 1.0000 1.0000
+   HW      HW   12-6 0.00000E+00 0.00000E+00 1.0000 1.0000 1.0000
+close
--- a/Data/Trajectories/DL_Poly/FIELD_cumen
+++ b/Data/Trajectories/DL_Poly/FIELD_cumen
+Automatic FIELD created for 1 molecule of Cumene              
+units kJ
+molecules 1
+Cumene              
+nummols 1
+atoms  21
+CB       12.0110   -0.1150     1     0
+CB       12.0110   -0.1150     1     0
+CB       12.0110   -0.1150     1     0
+CB       12.0110   -0.1150     1     0
+CS       12.0110    0.0000     1     0
+CB       12.0110   -0.1150     1     0
+C3       12.0110   -0.0600     1     0
+C1       12.0110   -0.1800     1     0
+C1       12.0110   -0.1800     1     0
+HR        1.0080    0.0600     1     0
+HR        1.0080    0.0600     1     0
+HR        1.0080    0.0600     1     0
+HR        1.0080    0.0600     1     0
+HR        1.0080    0.0600     1     0
+HR        1.0080    0.0600     1     0
+HB        1.0080    0.1150     1     0
+HB        1.0080    0.1150     1     0
+HB        1.0080    0.1150     1     0
+HB        1.0080    0.1150     1     0
+HB        1.0080    0.1150     1     0
+HR        1.0080    0.0600     1     0
+bonds  21
+harm    7   8   2594.0801   1.526
+harm    7   9   2594.0801   1.526
+harm    5   7   2652.6560   1.520
+harm    4   5   3924.5920   1.400
+harm    5   6   3924.5920   1.400
+harm    1   2   3924.5920   1.400
+harm    1   6   3924.5920   1.400
+harm    2   3   3924.5920   1.400
+harm    3   4   3924.5920   1.400
+harm    1  19   3071.0559   1.080
+harm    2  18   3071.0559   1.080
+harm    3  17   3071.0559   1.080
+harm    4  16   3071.0559   1.080
+harm    6  20   3071.0559   1.080
+harm    8  13   2845.1201   1.090
+harm    8  14   2845.1201   1.090
+harm    8  15   2845.1201   1.090
+harm    9  10   2845.1201   1.090
+harm    9  11   2845.1201   1.090
+harm    9  12   2845.1201   1.090
+harm    7  21   2845.1201   1.090
+angles  36
+harm    1   2   3    527.1840  120.000
+harm    2   1   6    527.1840  120.000
+harm    2   3   4    527.1840  120.000
+harm    1   6   5    527.1840  120.000
+harm    3   4   5    527.1840  120.000
+harm    4   5   6    527.1840  120.000
+harm    4   5   7    585.7600  120.000
+harm    6   5   7    585.7600  120.000
+harm    1   2  18    292.8800  120.000
+harm    1   6  20    292.8800  120.000
+harm    2   1  19    292.8800  120.000
+harm    2   3  17    292.8800  120.000
+harm    3   2  18    292.8800  120.000
+harm    3   4  16    292.8800  120.000
+harm    4   3  17    292.8800  120.000
+harm    6   1  19    292.8800  120.000
+harm    5   4  16    292.8800  120.000
+harm    5   6  20    292.8800  120.000
+harm    5   7   8    527.1840  114.000
+harm    5   7   9    527.1840  114.000
+harm    8   7   9    334.7200  109.500
+harm    5   7  21    418.4000  109.500
+harm    8   7  21    418.4000  109.500
+harm    9   7  21    418.4000  109.500
+harm    7   8  13    418.4000  109.500
+harm    7   8  14    418.4000  109.500
+harm    7   8  15    418.4000  109.500
+harm    7   9  10    418.4000  109.500
+harm    7   9  11    418.4000  109.500
+harm    7   9  12    418.4000  109.500
+harm   10   9  11    585.7600  109.500
+harm   10   9  12    585.7600  109.500
+harm   11   9  12    585.7600  109.500
+harm   13   8  14    585.7600  109.500
+harm   13   8  15    585.7600  109.500
+harm   14   8  15    585.7600  109.500
+dihedrals  48
+cos     1   2   3   4     60.6680    180.0000      2.0000  0.50 0.50
+cos     3   2   1   6     60.6680    180.0000      2.0000  0.50 0.50
+cos     1   6   5   4     60.6680    180.0000      2.0000  0.50 0.50
+cos     3   4   5   6     60.6680    180.0000      2.0000  0.50 0.50
+cos     2   1   6   5     60.6680    180.0000      2.0000  0.50 0.50
+cos     2   3   4   5     60.6680    180.0000      2.0000  0.50 0.50
+cos     1   2   3  17     60.6680    180.0000      2.0000  0.50 0.50
+cos     2   1   6  20     60.6680    180.0000      2.0000  0.50 0.50
+cos     2   3   4  16     60.6680    180.0000      2.0000  0.50 0.50
+cos     3   2   1  19     60.6680    180.0000      2.0000  0.50 0.50
+cos     4   3   2  18     60.6680    180.0000      2.0000  0.50 0.50
+cos     6   1   2  18     60.6680    180.0000      2.0000  0.50 0.50
+cos     5   4   3  17     60.6680    180.0000      2.0000  0.50 0.50
+cos     5   6   1  19     60.6680    180.0000      2.0000  0.50 0.50
+cos     4   5   6  20     60.6680    180.0000      2.0000  0.50 0.50
+cos     6   5   4  16     60.6680    180.0000      2.0000  0.50 0.50
+cos    16   4   3  17     60.6680    180.0000      2.0000  0.50 0.50
+cos    17   3   2  18     60.6680    180.0000      2.0000  0.50 0.50
+cos    18   2   1  19     60.6680    180.0000      2.0000  0.50 0.50
+cos    19   1   6  20     60.6680    180.0000      2.0000  0.50 0.50
+cos     1   6   5   7     60.6680    180.0000      2.0000  0.50 0.50
+cos     3   4   5   7     60.6680    180.0000      2.0000  0.50 0.50
+cos     7   5   4  16     60.6680    180.0000      2.0000  0.50 0.50
+cos     7   5   6  20     60.6680    180.0000      2.0000  0.50 0.50
+cos     4   5   7   8      0.0000      0.0000      2.0000  0.50 0.50
+cos     4   5   7   9      0.0000      0.0000      2.0000  0.50 0.50
+cos     6   5   7   8      0.0000      0.0000      2.0000  0.50 0.50
+cos     6   5   7   9      0.0000      0.0000      2.0000  0.50 0.50
+cos     4   5   7  21      0.0000      0.0000      2.0000  0.50 0.50
+cos     6   5   7  21      0.0000      0.0000      2.0000  0.50 0.50
+cos     5   7   8  13      5.8576      0.0000      3.0000  0.50 0.50
+cos     5   7   8  14      5.8576      0.0000      3.0000  0.50 0.50
+cos     5   7   8  15      5.8576      0.0000      3.0000  0.50 0.50
+cos     5   7   9  10      5.8576      0.0000      3.0000  0.50 0.50
+cos     5   7   9  11      5.8576      0.0000      3.0000  0.50 0.50
+cos     5   7   9  12      5.8576      0.0000      3.0000  0.50 0.50
+cos    10   9   7  21      5.8576      0.0000      3.0000  0.50 0.50
+cos    11   9   7  21      5.8576      0.0000      3.0000  0.50 0.50
+cos    12   9   7  21      5.8576      0.0000      3.0000  0.50 0.50
+cos    13   8   7  21      5.8576      0.0000      3.0000  0.50 0.50
+cos    14   8   7  21      5.8576      0.0000      3.0000  0.50 0.50
+cos    15   8   7  21      5.8576      0.0000      3.0000  0.50 0.50
+cos     8   7   9  10      5.8576      0.0000      3.0000  0.50 0.50
+cos     8   7   9  11      5.8576      0.0000      3.0000  0.50 0.50
+cos     8   7   9  12      5.8576      0.0000      3.0000  0.50 0.50
+cos     9   7   8  13      5.8576      0.0000      3.0000  0.50 0.50
+cos     9   7   8  14      5.8576      0.0000      3.0000  0.50 0.50
+cos     9   7   8  15      5.8576      0.0000      3.0000  0.50 0.50
+finish
+vdw  21
+HB       HB        lj      0.125520  2.420000
+HB       HR        lj      0.125520  2.460000
+HB       CB        lj      0.191735  2.985000
+HB       C3        lj      0.186176  2.960000
+HB       C1        lj      0.186176  2.960000
+HB       CS        lj      0.191735  2.985000
+HR       HR        lj      0.125520  2.500000
+HR       CB        lj      0.191735  3.025000
+HR       C3        lj      0.186176  3.000000
+HR       C1        lj      0.186176  3.000000
+HR       CS        lj      0.191735  3.025000
+CB       CB        lj      0.292880  3.550000
+CB       C3        lj      0.284389  3.525000
+CB       C1        lj      0.284389  3.525000
+CB       CS        lj      0.292880  3.550000
+C3       C3        lj      0.276144  3.500000
+C3       C1        lj      0.276144  3.500000
+C3       CS        lj      0.284389  3.525000
+C1       C1        lj      0.276144  3.500000
+C1       CS        lj      0.284389  3.525000
+CS       CS        lj      0.292880  3.550000
+close
--- a/Data/Trajectories/DL_Poly/FIELD_felodipine
+++ b/Data/Trajectories/DL_Poly/FIELD_felodipine
--- a/Data/Trajectories/DL_Poly/FIELD_methanol
+++ b/Data/Trajectories/DL_Poly/FIELD_methanol
+methanol
+units kJ
+molecules 1
+methanol 
+nummols 1000
+atoms   6
+CT       12.0110    0.1450     1     0
+OH       15.9990   -0.6830     1     1
+HO        1.0080    0.4180     1     0
+HC        1.0080    0.0400     1     0
+HC        1.0080    0.0400     1     0
+HC        1.0080    0.0400     1     0
+constraints   5
+1   2     1.410
+1   4     1.090
+1   5     1.090
+1   6     1.090
+2   3     0.945
+angles   7
+harm    4   1   5    138.0720  107.800
+harm    4   1   6    138.0720  107.800
+harm    5   1   6    138.0720  107.800
+harm    1   2   3    230.1200  108.500
+harm    2   1   4    146.4400  109.500
+harm    2   1   5    146.4400  109.500
+harm    2   1   6    146.4400  109.500
+dihedrals   3
+cos3    3   2   1   4      0.0000      0.0000      1.8828  0.50 0.50
+cos3    3   2   1   5      0.0000      0.0000      1.8828  0.50 0.50
+cos3    3   2   1   6      0.0000      0.0000      1.8828  0.50 0.50
+finish
+vdw  10
+CT       CT        lj      0.276144  3.500000
+CT       OH        lj      0.443188  3.304542
+CT       HO        lj      0.000000  0.000000
+CT       HC        lj      0.186176  2.958040
+OH       OH        lj      0.711280  3.120000
+OH       HO        lj      0.000000  0.000000
+OH       HC        lj      0.298797  2.792848
+HO       HO        lj      0.000000  0.000000
+HO       HC        lj      0.000000  0.000000
+HC       HC        lj      0.125520  2.500000
+close    
--- a/Data/Trajectories/DL_Poly/FIELD_water_with_gradients
+++ b/Data/Trajectories/DL_Poly/FIELD_water_with_gradients
+TIP4P/2005 heavy water model
+UNITS kJ
+
+MOLECULES 1
+TIP4P2005 water
+NUMMOLS 4000
+ATOMS 4
+OW           15.999         0.0000   1    0    1
+HW            2.014         0.5564   2    0    1
+OM            0.000        -1.1128   1    0    1
+RIGID BODIES 1
+    4    1    2    3    4
+FINISH
+VDW 1
+OW      OW        lj     0.7749     3.1589  
+CLOSE
+
+!From Abascal (2005): 
+!
+! V = 4E*((s/r)^12-(s/r)^6) with s = 3.1589  A
+!                                E = 93.2 K = 0.77490787 kJ/mol
+!
+!Water geometry: d(OH) = 0.9572 A, angle(HOH) = 104.52, d(OM) = 0.1546 A
--- a/Data/Trajectories/DL_Poly/FIELD_water_with_velocities
+++ b/Data/Trajectories/DL_Poly/FIELD_water_with_velocities
+TIP4P/2005 heavy water model
+UNITS kJ
+
+MOLECULES 1
+TIP4P2005 water
+NUMMOLS 4000
+ATOMS 4
+OW           15.999         0.0000   1    0    1
+HW            2.014         0.5564   2    0    1
+OM            0.000        -1.1128   1    0    1
+RIGID BODIES 1
+    4    1    2    3    4
+FINISH
+VDW 1
+OW      OW        lj     0.7749     3.1589  
+CLOSE
+
+!From Abascal (2005): 
+!
+! V = 4E*((s/r)^12-(s/r)^6) with s = 3.1589  A
+!                                E = 93.2 K = 0.77490787 kJ/mol
+!
+!Water geometry: d(OH) = 0.9572 A, angle(HOH) = 104.52, d(OM) = 0.1546 A
--- a/Data/Trajectories/DL_Poly/HISTORY_Water
+++ b/Data/Trajectories/DL_Poly/HISTORY_Water
--- a/Data/Trajectories/DL_Poly/HISTORY_cumen
+++ b/Data/Trajectories/DL_Poly/HISTORY_cumen
--- a/Data/Trajectories/DL_Poly/HISTORY_felodipine
+++ b/Data/Trajectories/DL_Poly/HISTORY_felodipine
--- a/Data/Trajectories/DL_Poly/HISTORY_methanol
+++ b/Data/Trajectories/DL_Poly/HISTORY_methanol
--- a/Data/Trajectories/DL_Poly/HISTORY_water_with_gradients
+++ b/Data/Trajectories/DL_Poly/HISTORY_water_with_gradients
--- a/Data/Trajectories/DL_Poly/HISTORY_water_with_velocities
+++ b/Data/Trajectories/DL_Poly/HISTORY_water_with_velocities
--- a/README.md
+++ b/README.md
-# MDANSE
 MDANSE (Molecular Dynamics Analysis for Neutron Scattering Experiments) is a python library/application for analysis molecular dynamics simulation data
+
+This is nMoldyn-3.0.12, an interactive program for the
+analysis of Molecular Dynamics trajectories. This program is
+copyrighted but free to use for anyone under the CeCILL license,
+see the file LICENSE for details.
+
+nMoldyn should work with all major variants of Unix, including Linux
+and MacOSX and Windows. There is little system-specific code in nMoldyn 
+itself, so porting nMoldyn to other systems should be straightforward.
+However, we cannot provide any support for this.
+
+If you have any questions about nMoldyn that are not answered on the
+Web page mentioned above, please contact the authors.
+
+
+Eric Pellegrini
+Calcul Scientific
+Institut Laue Langevin
+6 Rue Jules Horowitz
+38042 Grenoble
+France
+E-Mail: pellegrini@ill.fr
+
+Konrad Hinsen
+Centre de Biophysique Moleculaire (CNRS)
+Rue Charles Sadron
+45071 Orleans Cedex 2
+France
+E-Mail: hinsen@cnrs-orleans.fr
+
+Gerald Kneller
+Centre de Biophysique Moleculaire (CNRS)
+Rue Charles Sadron
+45071 Orleans Cedex 2
+France
+E-Mail: kneller@cnrs-orleans.fr
+
+Step 1: Prerequesites
+=====================
+
+Before installing nMOLDYN make sure that the following components are installed
+and configured properly:
+
+	-Tcl and Tk libraries version >= 8.4
+
+	-Python 2.4 or higher
+	-numpy version >= 1.2
+	-matplotlib version >= 0.98
+	-pyro version >= 3.9
+	-Scientific version >= 2.8
+	-MMTK version >= 2.6.1
+
+    -NetCDF library version >= 3.6.1
+     To check for that, in a terminal, type
+
+         python -c 'import Scientific.IO.NetCDF'
+
+     If you get no error message NetCDF is likely to be properly installed and 
+     configured on your system.
+
+
+Step 2: installation
+====================
+
+In a terminal, type the following instructions in the directory where you untared
+the nMOLDYN archive:
+
+    cd nMOLDYN-3.X.Y
+    python setup.py build
+    python setup.py install
+
+The last command may require administrator privileges.
+
+
+Step 3: running nMOLDYN
+=======================
+
+Once the installation is completed run nMOLDYN by typing
+
+	./nMOLDYNStart.py
+	
+in your Python binaries directory.
+
+In the future, you should create an alias/shortcut for that script in order to not 
+disrupt any component of that sensitive directory.
+
+WARNING:
+========
+
+If the version of Scientific used to run nMOLDYN is the 2.9.0, small changes has 
+to be performed in order to use nMOLDYN in parallel mode via a Pyro server.
+
+The changes are the following:
+
+FILE    : MasterSlave.py
+LOCATION: Scientific installation directory
+
+REPLACE
+
+def getMachineInfo():
+    import os
+    sysname, nodename, release, version, machine = os.uname()
+    pid = os.getpid()
+    return "PID %d on %s (%s)" % (pid, nodename, machine)
+
+BY
+
+def getMachineInfo():
+    import os
+    import platform
+    sysname, nodename, release, version, machine, processor = platform.uname()
+    pid = os.getpid() 
+    return "PID %d on %s (%s)" % (pid, nodename, machine)
+
+If you are not familiar with the Python installed modules file structure, you
+can find the path for Scientific directory by running the following command 
+within the Python interpreter:
+
+import Scientific
+print Scientific.__path__[0]
+
+KNOWN BUGS:
+===========
+
+    - Bug with tk >= 8.5 on Linux (Fedora, Suse, Ubuntu): when using a tkMessageBox, if you click 'Yes' 
+    the answer will be the same as 'No'! In nMOLDYN, you will experience this bug at the end of an 
+    analysis when you can decide to plot the results just after the analysis. Whatever is your decision 
+    ('Yes' or 'No'), no plot will be displayed.
+    
+    Here is the proposed patch (http://bugs.python.org/issue4961):
+    
+    Index: Lib/lib-tk/tkMessageBox.py
+    ===================================================================
+    --- Lib/lib-tk/tkMessageBox.py	(revision 73494)
+    +++ Lib/lib-tk/tkMessageBox.py	(working copy)
+    @@ -70,11 +70,13 @@
+         if title:   options["title"] = title
+         if message: options["message"] = message
+         res = Message(**options).show()
+    -    # In some Tcl installations, Tcl converts yes/no into a boolean
+    +    # In some Tcl installations, yes/no is converted into a boolean.
+         if isinstance(res, bool):
+    -        if res: return YES
+    +        if res:
+    +            return YES
+             return NO
+    -    return res
+    +    # In others we get a Tcl_Obj.
+    +    return str(res)
+ 
+     def showinfo(title=None, message=None, **options):
+         "Show an info message"
+    
+