We (Pal+Bikash) have created a cross-linked epoxy structure from scratch using the following procedure:
(1) creation of coarse-grained structure
(2) cross-linking of coarse grained structure using LAMMPS
(3) fine-grain of of coarse-grained structure by custom code (hardest bit)
Our versions with big-fixes are explained:
1.0 pristine
2.0 bugs resolved: DGEBA was not being mapped properly to coarse-grained molecule (j-->j-4: error); pbc during cross-linking caused bonds to form across boundaries (grave error)
2.1 hideous bug: 'possible pairs problem' due to faulty if condition (which was looking for a zero for end.of.line and which did not exist for saturated binder atom)
Tuesday, June 14, 2011
Tuesday, December 7, 2010
Hybrid lammps functional
We succeeded in implementing a hybrid potential for a functionalized CNT, airebo for the nano-tube and class2 for the functional group. The secret lay in defining the sp3 carbon on the nano-tube to be a sp2 carbon atom, this however should not cause a problem as airebo is perfectly equipped to handle diamond(sp3) and CNT(sp2) atoms.
Besides another imp. fact that was ignored earlier was declaring the airebo params as 'NULL' for the atoms not being modeled by airebo. We had numerous problems owing to mis-formatting of the data file.
We must still look for breakable bond parameters for the polymer.
Besides another imp. fact that was ignored earlier was declaring the airebo params as 'NULL' for the atoms not being modeled by airebo. We had numerous problems owing to mis-formatting of the data file.
We must still look for breakable bond parameters for the polymer.
Sunday, November 21, 2010
airebo lammps real units
I had a hard time looking for the 'real' units version of AIREBO in lammps, so i made one myself and its available for all at https://sites.google.com/site/mechapple1501/pages/CH.airebo_real?attredirects=0&d=1
Cheers
Cheers
Sunday, November 14, 2010
Back with functionalised CNTs
Its been quite a while but its never too late to resume.
I've been trying to simulate a CNT with airebo and LAMMPS. Got an unstable system for atom_style molecular. So i changed it to atomic and (whoopie!) got a stable one. I still have to figure out how i should use airebo in a hybrid scheme.
Besides, the potential database provided by Medea Lammps isn't helping much at all. It seems to be missing some basic parameters. Until i can sort them out, i will have to use free LAMMPS. Luckily, i found a peptide example in the lammps folder which contained params for a lot of organic bonds. I guess I'll have to use that.
I've been trying to simulate a CNT with airebo and LAMMPS. Got an unstable system for atom_style molecular. So i changed it to atomic and (whoopie!) got a stable one. I still have to figure out how i should use airebo in a hybrid scheme.
Besides, the potential database provided by Medea Lammps isn't helping much at all. It seems to be missing some basic parameters. Until i can sort them out, i will have to use free LAMMPS. Luckily, i found a peptide example in the lammps folder which contained params for a lot of organic bonds. I guess I'll have to use that.
Thursday, January 8, 2009
Thursday, 8th January 09, 1900 hrs
The threaded program for the indentation is 70% complete and its up and running. L-D curve is observed to be sinusoidal at low indenter speeds and distances far away from the surface.
2 new concepts have been added:
Large list - this additional list has been added to improve speeds by providing the environment list where neighbor atoms will be identified
Append list - increases speed dramatically by modifying the previous list and not making a new one every time the makelist() function is called]
SegFaults (SF) can now be circumvented, thanks to GDB.
SF tips: Always remember to create output folder
2 new concepts have been added:
Large list - this additional list has been added to improve speeds by providing the environment list where neighbor atoms will be identified
Append list - increases speed dramatically by modifying the previous list and not making a new one every time the makelist() function is called]
SegFaults (SF) can now be circumvented, thanks to GDB.
SF tips: Always remember to create output folder
Wednesday, December 17, 2008
Wednesday, 17th December 08, 1900 hrs
Apparently the trip to SERC, IISc has been fruitful. Even though the field of parallel processing maybe intensely convoluted and even after facing the atrocities of Linux, I have managed to retain my nerves. It was evident that programming using threads and MPIs are two completely different approaches to PP but the problem at hand requires extensive knowledge of both.
We shall be using multiple clusters each having multiple cores which makes the job interesting, if not frightening. I was exposed to graph partitioning and realised that METIS made my job a LOT easier. All i had to do was to generate the graph containing a list of expected interactions every atom would be having, which was a piece of cake considering the program structure. Incorporating the pmetis code into my existing program took a lot of time: linking it to its libraries was a major bottleneck, eventually circumvented by running my original code itself from the metis test folder. I also learnt gcc and g++ are disturbingly different, and had to change my .cpp to a .c as the metis code was written in C.
After writing (copying :D ) a program to compute the value of pi, I got a clearer idea of POSIX threads. Now all I have to do, is to implement POSIX threads on my MD code, which is going to be a helluva job. And wait! I haven't even begun on cluster programming and MPI, so till then i wont be using METIS.
We shall be using multiple clusters each having multiple cores which makes the job interesting, if not frightening. I was exposed to graph partitioning and realised that METIS made my job a LOT easier. All i had to do was to generate the graph containing a list of expected interactions every atom would be having, which was a piece of cake considering the program structure. Incorporating the pmetis code into my existing program took a lot of time: linking it to its libraries was a major bottleneck, eventually circumvented by running my original code itself from the metis test folder. I also learnt gcc and g++ are disturbingly different, and had to change my .cpp to a .c as the metis code was written in C.
After writing (copying :D ) a program to compute the value of pi, I got a clearer idea of POSIX threads. Now all I have to do, is to implement POSIX threads on my MD code, which is going to be a helluva job. And wait! I haven't even begun on cluster programming and MPI, so till then i wont be using METIS.
Thursday, December 11, 2008
Thursday, 11th December 08, 2315 hrs
Much, much better shape stability observed with the EAM model. A 10x10x10 cube was simulated and allowed to stabilize. Even after shrinking and edge rounding, the basic shape of the cube was maintained. Thank god.
Strictly as per Joe's instructions, we have decided to simulate a larger cube and observe system energies. I am hoping to get constant total energy after stabilization. We might even run a simulation or 10 days or more.
Strictly as per Joe's instructions, we have decided to simulate a larger cube and observe system energies. I am hoping to get constant total energy after stabilization. We might even run a simulation or 10 days or more.
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