=== This is the readme file ===
=== June 16 2015 ==============
After buying the Intel FORTRAN compiler for Visual Studio, I hope to build versions of Packmol for
the Windows platform - x86 and x64.
I have added a Windows-x64 version of the ORIGINAL Packmol here as a test. I will add one of my modified
=== I have replaced the msi2lmp individual file downloads with a tar file and I have done the same for the packmol modifications. The documentation for building the software
=== was updated as well. Please contact me when something is not working and I will respond as soon as I can.
=== Thank you!
=== I HAVE UPLOADED THE CORRECT COPY OF LIBRARY.ZIP. I HAVE HAD THE INCORRECT COPY ON THE SITE SINCE THE BEGINNING. PLEASE DOWNLOAD THE CORRECT COPY
=== THE NANOENGINEER-1 WITH THE CFF91 FORCE FIELD SHOULD WORK AS EXPECTED.
=== NOTE: Nanoengineer-1.net has been down for a while and the owner has gotten it back up!
You can download NanoEngineer-1 for Windows, MAC and Linux from this site. My changes only apply to the Windows version of the software - for now.
=== FOR THE TIME BEING PLEASE DOWNLOAD THE msi2lmp.tar.gz FILE IF YOU WANT TO BUILD ON CYGWIN AND PERHAPS LINUX. IF YOU WANT TO BUILD UNDER
=== WINDOWS JUST CREATE A PROJECT FILE AND USE THE SOURCE CODE TO BUILD AN EXECUTABLE. ONCE YOU HAVE THE msi2lmp executable you can
=== name it ne2lmp so it is different from the msi2lmp executable. AT THIS POINT IN TIME I WILL CONSTRUCT AN ne2lmp executable so it is a seperate
=== Apparently the MSI2LMP tool is still being maintained!!! I have to determine if I can submit my changes for inclusion into
=== the existing code base or just create a new tool from the source I started with.
=== Modifying the current baseline of MSI2LMP with my changes will require more work than copying my changed and new files over top
=== of the current baseline, which could change over time.
=== I apologize for not providing the global.i file earlier for the PACKMOL modifications!!! This will allow the changes to compile and link.
It has come to my attention that there could be a problem with registering at the NANOREX, Inc. website to download the
original NanoEngineer-1. This is needed to apply the library.zip file to. I am uploading the file since I registered
a long time ago on the site. My changes only apply, for now, to the Windows version. I am also supplying the source code
and the MAC versions of the application. I will be working to make my modifications work on MAC and Linux as time goes on.
I am sorry this is a problem.
=== IT IS IMPORTANT TO NOTE THAT THE THREE SOFTWARE APPLICATIONS ARE USED IN A SERIAL MANNER.
===1. ONE CREATE TEMPLATES OF MOLECULES USING NANOENGINEER-1. YOU WILL HAVE ONE OR MORE MOLECULAR MACHINE PART FILES
=== (mmp) EACH WITH A SEPERATE MOLECULE. DON'T FORGET TO MINIMIZE ITS ENERGY.
===2. CREATE THE *.INP FILE FOR PACKMOL. THE EXAMPLES DIRECTORY NOW CONTAINS EXAMPLES OF AN OLIGOMER AND WATER
=== AND A *.INP FILE FOR PACKMOL - E.G. SQUARECFF91.INP. BY RUNNING WITH THE *.INP FILE YOU CAN CREATE THE DGEBAWATER.MMP FILE.
=== PLEASE SEE THE EXAMPLES.
===3. RUN THE MSI2LMP TO CONVERT DGEBAWATER.MMP INTO A LAMMPS GEOMETRY INPUT FILE. THIS PROCESS REQUIRES THE NUMERIC CFF91
=== FILE IN THE NUMERIC CFF91 DIRECTORY. THIS REQUIRES SETTING UP THE BIOSYM_LIBRARY ENVIRONMENT VARIABLE UNDER YOUR OPERATING SYSTEM.
=== THE cff91_cff91v.frc file MUST BE IN THE DIRECTORY YOU POINT TO WITH THIS ENVIRONMENT VARIABLE.
=== I HAVE SEEN MANY DOWNLOADS AND WOULD LIKE VERY MUCH TO HEAR BACK ABOUT PROBLEMS AND ISSUES
=== PLEASE RESPOND THROUGH THE SOURCE FORGE SITE AND I WILL RESPOND VIA GMAIL
=== gmail: claudevms AT gmail DOT com
=== 9/9/2012 - Resumed uploading source files for this project ===
=== 9/12/2012 -MODIFIED README FILE
===10/04/2012 -ADDED THE MSI2LMP.EXE file for WINDOWS. This was build using VC++ in VS 2008
=== -MSI2LMP.EXE converts the MMP file from either NE-1 or the modified PACKMOL into
=== a LAMMPS Geometry Input File. You must use the force field file located in the NUMERIC
=== CFF91 directory. Please download and read the directions of MSI2LMP in the LAMMPS distribution
=== to setup the environment variables!!!
===10/04/2012 -ADDED an example file to the EXAMPLES directory. square3cff91.mmp is a molecular machine part file
=== I created by hand in NE-1. It is a cross-linked oligomer consisting of 4 IPD molecules and 9 DGEBA
=== molecules. The configuration of the oligomer was shamlessly borrowed from Tack & Ford who
=== developed this configuration for their MD simulations.
===10/04/2012 -ADDED suggestion on how to run PACKMOL on Windows using the CYGWIN/MING build executable.
===10/04/2012 -ADDED CYGWIN PACKMOL executable to the Windows executables directory including the CYGWIN
=== the DLLs needed for the Windows system directory. I suggest installing CYGWIN and trying out a
=== fantastic and masterful work of opensource!!! I put the DLLs in here really to provide the names
===10/10/2012 I APOLOGIZE FOR SPECIFYING SERVICE PACK 1 FOR WINDOWS 7. THERE IS A DLL ISSUE WITH SP1 AND YOU
=== CANNOT RUN THE MODIFIED NANOENGINEER-1 UNDER SP1!!!
===10/10/2012 I HAVE DISCOVERED RECENTLY THAT THE NANOENGINEER-1 WIKI SITE IS DOWN. THIS SITE IS CRITICAL TO
=== TO CREATING A DEVELOPMENT VERSION OF THE NANOENGINEER-1 SOFTWARE AND RUNNING IT INSIDE WINGIDE.
===10/10/2012 I'M WORKING ON TWO PDF DOCUMENTS ONE IS A BUILD AND INSTALLATION AND THE SECOND IS A SCIENCE DOCUMENT
=== EXPLAINING HOW TO BUILD AN MD CELL AND THE LAMMPS SIMULATIONS USED TO CALCULATE DENSITY AND GLASS
=== TRANSITION TEMPERATURE
===10/12/2012 I have added a draft Build and Installation PDF to the documentation directory
===10/12/2012 I have updated my slides for my master's defense and uploaded it to show the initial operational capability (IOC) of
=== Molecular Dynamics Studio
===10/16/2012 Added PACMOL input files squarecff91.mmp and water.mmp. Added squarecff91.inp, which is the PACMOL command file
=== if you place all files in a common directory you can run packmol at the command line packmol squarecff91.inp
=== and generate the dgebawater.mmp file. You can use NanoEngineer-1 to look at the final system containing 5 oligomers and
=== 20 water molecules. The dgebawater.mmp in in the PACKMOL out files directory.
===10/17/2012 Added very draft software instructions into the documentation directory
WARNING: I BELIEVE ALL FILES HAVE BEEN UPLOADED!!! YOU MUST DOWNLOAD ALL FILES FOR
NANOENGINEER-1, PACKMOL AND MSI2LMP INORDER TO EFFECTIVELY USE THE SOFTWARE.
PLEASE SUBMIT TROUBLE TICKETS OR EMAIL ME AND I WILL RESPOND WITH FIXES AS I CAN.
NOTE: THE SOFTWARE DOES NOT CONTAIN ANY COMPASS FORCE FIELD INFORMATION. THE PROJECT STARTED
USING THE PUBLISHED COMPASS FORCEFIELD DATA FROM THE SUN PAPERS. ONCE IT WAS DETERMINED THAT COMPASS COULD
NOT BE USED IN ITS ENTIRETY, CFF91 WAS USED. REFERENCES TO COMPASS PUBLISHED AND UNPUBLISHED IN NANOENGINEER-1 ARE
EXAMPLES OF HOW MULTIPLE FORCEFIELDS COULD BE ADDED TO THE SOFTWARE. ANY FORCEFIELD EXISTS AS A COLLECTION
OF ATOM TYPE SYMBOLS WHILE ONE WOULD REQUIRE THE FORCEFIELD FILE FROM THE OWNER. I COULD HAVE REFERENCED
AMBER OR OTHER FORCEFIELDS IN THE SELECTION WIDGET.
NanoEngineer-1 can be downloaded from http://www.nanoengineer-1.com/content/
You must create an account to download NanoEngineer-1 at the Nanorex site
Go to this URL for details: http://www.nanoengineer-1.net/mediawiki/index.php?title=Online_Readme
Once you install NanoEngineer-1 on your Windows XP, Vista or Windows 7 operating system
you must place the library.zip file into the C:\Program File(x86)\Nanorex\NanoEngineer-1v1.1.1\program
directory. First rename the existing library.zip if you want to return to the original software.
PACKMOL can be downloaded from http://www.ime.unicamp.br/~martinez/packmol/
You must copy the modified files into the directory where you install PACKMOL and follow the PACKMOL
build instructions. I created a packmolnew.f file so I could debug the program easierly. It uses > and <
to direct file input output and that conflicts with DDD/gdb. You may want to build PACKMOL
under CYGWIN or MING - I found that easy. NOTE: once you build PACKMOL executable under MING or CYGWIN you can
run it under windows without CYGWIN or MING by adding the following CYGWIN libraries to the Windows
system directory: cygg_s-1.dll, cyggfortran-3.dll cygwin1.dll. The PACKMOL executable will look for these
libraries in order to execute on a plain Windows platform.
MSI2LMP can be downloaded as part of the LAMMPS molecular dynamics software from http://lammps.sandia.gov/
The LAMMPS software is distributed as a tar.gz file. Follow the directions for downloading, decompressing
and untaring the software. A directory is created containing all LAMMPS software. The MSI2LMP software
is located in ../lammps-ddmmmyy/tools/msi2lmp/src. Copy the modified files into the installation directory
above. Save the original files if you need them.
MSI2LMP can be built for UNIX/Linux/OSX or Windows. Building the software for Windows requires creating a
project file in Visual Studio and adding the source to the project. Building for Unix/Linux/OSX requires
running the make for the platform.
Running the software
1. Run NanoEngineer-1 and create indivdual files for all the specific molecules you want to place
in the MD cell. There will be one MMP file per molecule.
2. After reading the PACKMOL user manual create a PACKMOL input file that contains references to
the molecules created in step 1 and the number of each molecules you want in the MD cell. PACKMOL
will create a single MMP file containing the MD cell.
3. Run the MSI2LMP program using the MMP file created by PACKMOL. This creates a LAMMPS geometry input file
ready for simulation.
SAW - self avoiding walk - which is still in development will be a tool to build MD cells using molecule templates created
from templates created in NanoEngineer-1. The software is being developed in C++ and will eventually integrate LAMMPS
via the callable interface. The goal is to have a software tool to support the creation of crosslinking via a dynamic
mechanism where molecules move over time and are "reacted" with one another based on rules the user defines.
More and detailed information is to follow...