Differences

This shows you the differences between two versions of the page.

--- classical_md [2010/06/22 13:03]
zdech
+++ classical_md [2011/02/18 13:13]
@@ Line 1: / Line 1: @@
- --- //[[chrom@fzu.cz|Zdenka Chromcova]] 2010/03/18 11:23//
-====== Using: ======
-===== Switching the classic MD on/off =====
-The using of classic potential could be switched on/off in file **fireball.in** :
-  * the implicit settings is off: iclassMD is not defined in fireball.in or iclassicMD = 0
-  * classic MD on: iclassicMD = 1
-===== Settings of parameters for classic MD =====
-in directory Cdata are two types of files:
-  - Cdata/usePotential.in //(define parameters of simulation)//
-  - Cdata/NAME-OF-POTENTIAL-DEFINED-IN-FILE-ABOVE.dat //(defines the parameters of potential)//
-===== usePotential.in =====
-In this file is defined which potential will be used and other parameters used in classical MD only.
-    * **Defines __which potential__ will be used**
-Format of file usePotential.in:
-    all Lennard-Jones
-or there could be defined potential for each pair: usePotential.in //(not useful at this moment)//:
-    H-H Lennard-Jones
-    Si Lennard-Jones
-    Si-H Lennard-Jones
-//**Note:** all pair potentials have to be of the same type. Thus this second type of definition of potential is not very usefull at this moment.//
-In the directory Cdata have to exist file with parameters of potential with name NAME-OF-POTENTIAL.dat (in case above the program will look for file Lennard-Jones.dat).
-  * **Defines __frequency of outputs__ in MD simulation.**
-The implicit value is each 1000th cycle. The example of the definition:
-    freq_of_outputs 100
-===== Files with potentials =====
-The parameters of potential is defined in files with name: Cdata/NAME-OF-POTENTIAL.dat . The string NAME-OF-POTENTIAL have to match with string which define potential in file **usePotential.in** .
-In this file are parameters for pair potential for different types of atoms in shape: Atom1-Atom2  params = [ params separate by comas ] . Comments starts with character "#". The example for for Lennard-Jones potential is below:
-===    Lennard-Jones.dat: ===
-    #                   epsilon         ro          cutoff
-    # shape of potential( 4epsilon( (ro/r)**12 - 2(ro/r)**6) cutoff = 2.5 ro/2**(1/6)
-    H-H     params = [      2   ,       2.4     ,   9.35 ]
-    Si-Si   params = [      2   ,       1.4     ,   9.35 ]
-    Si-H    params = [      2   ,       1.9     ,   9.35 ]
-In these files could be defined more pairs than will be used in simulations. If the program do not find an pair defined in basisfile it ends with error message which pair is missing.
-==== Supported potentials ====
-At this moment there is only Lennard-Jones potential. There going to be addaed also RGL, EAM, MEAM and Tersoff potential.
-List of potentials:
-  * Lennard-Jones
-  * [[RGL potential]]
-====== Example ======
-The input files for a nanocluster of Pd13 is here: {{:pd.tar.gz|}}. The initial configuration (in.bas file) is in global minima according a program for MD of Ficcardo Ferrando using the same shape of RGL potential with the same parameters. The value of total energy in the global minima is -42.09318eV (according Riccardo's program). The shape of the cluster in GM is [[http://nanosurf.fzu.cz/wiki/lib/exe/fetch.php?media=pd_gm.png|icosahedral]].
-====== New files and changes in Fireball: ======
-===== New files =====
-Because of classic MD there were added these files:
-  * DASSEMBLERS/getforces_classic.f90
-  * READFILES/readdata_classicMD.f90
-  * MODULES/classicMD.f90
-  * MODULES/classicMEAMforces.f90 //routines used in empirical potentials//
-  * NEIGHBOR/find_neigh_max_class.f90
-  * INITIALIZERS/init_getforces.f90 //assignment of the pointer on the function which give the force (one of dft or the classic)//
-  * DASSEMBLERS/getforces_classic_RGL.f90
-  * DASSEMBLERS/getforces_classic_Tersoff.f90 //(not yet in use)//
-=== Details of files: ===
-== DASSEMBLERS/getforces_classic.f90 ==
-Here is defined the main procedure for classic_forces which call the relevant procedure for given potential. The "relevant procedures" will be defined in the individual files in future.
-== MODULES/classicMD.f90 ==
-Definition of global variable "*Potential", user-defined types and interface for subroutines and functions.
-== NEIGHBORS/neighbors.f90, MODULES/neighbor_map.f90, ALLOCATE/allocate_neigh.f90, NEIGHBOR/find_neigh_max_class.f90, INITIALIZERS/initbasics.f90 ==
-if iclassicMD = 1 there is allocate and initialized also new arrays:
-    !CHROM neighbor for classical MD simulation (MODULES/neighbor_map.f90)
-    integer :: neigh_max_class = 0 !size of arrays
-    integer, dimension(:,:),   allocatable     ::  neigh_classic
-    integer, dimension(:),     allocatable     ::  neighn_classic
-    integer, dimension(:,:),   allocatable     ::  neigh_b_classic
-    !END CHROM
-The arrays of quantum neighbors are kept unchanged to should be used in future eventually (i.e. there should be implemented the combination of classic and quantum simulation)
-===== Changes in existing files =====
-The code which was added or changed because of classic MD (by Zdenka Chromcova) is between tags:
-  * begin: !CHROM
-  * end:   !END CHROM
-**The list of files which were changed:**
-  * Makefile
-  * LOOPS/main_loop_MD.f90 //( defined loop for classic MD )//
-  * INITIALIZERS/initbasics.f90 //(if iclassicMD = 1: added filling of classical neighbors)//
-  * ALLOCATE/allocate_neigh.f90 //(if iclassicMD = 1:allocation of classical neighbors)//
-  * MODULES/neighbor_map.f90 //(added definition of classical neighbors)//
-  * MODULES/options.f90
-  * NEIGHBORS/neighbors.f90 //(added actualization of classicl neighbor if iclassicMD = 1. Note: if iclassicMD>1 both classic and quantum arrays for neighbors are actualized)//
-  * READFILES/readparam.f90
-  * READFILES/readdata.f90
-  * MD/move-ions.f90 //(
-A) added variable vmax (maximum if the velocity) and in case that vmax*dt>2 && iclassicMD>0 it break the program.
-B) if iclassicMD>0 the outputs are with period given in userPotential.in
-C) some do-loops was joined together (because of computer time))//
-i.e. this (2x3xN loops)
-  vatom(:,1:natoms) = vatom(:,1:natoms)*vscale
-  xdot(1,:,1:natoms) = xdot(1,:,1:natoms)*vscale
-was rewritten as (Nx3 loops):
-  do iatom = 1, natoms
-    do k=1,3
-      vatom(k,iatom) = vatom(k,iatom)*vscale
-      xdot(1,k,iatom) = xdot(1,k,iatom)*vscale
-    enddo
-  enddo
-  * DASSEMBLERS/getforces.f90 //Not more used. Now getforces is not the function, but the pointer on the function (defined in MODULES/forces.f90).//
-  * MODULE/forces.f90 //(added row: "procedure (), pointer :: getforces" )//
-----
-[[http://nanosurf.fzu.cz/people/zdenka/public/fireball_chro.tar.gz|Download (a bit old verion: January 2010)]]
-----
-====== ToDo list (zdenka) ======
-  * <del> output on the screen and into the files is not done in each step (some intervals if iclassicMD==1, definition in usePotential.in)</del>
-  * <del>[[http://nanosurf.fzu.cz/wiki/doku.php?id=fortran|pointer on subroutines]] which calculates the forces (not the case statement)</del>
-  * <del>if velocity*dt>2 then it write out the warrning that dt is too small (in case iclassicMD>0 only)</del>
-  * made better structure of type(POTENTIALTYPE) //(One type of potential for all atoms - delete the components ptype and type in the definition of type(POTENTIALTYPE) )//
-  * <del>add RGL potencial (the total energy of cluster is the same as the code of Riccardo Ferrando gives)</del>
-  * verify the biatomical clusters! (comape with Riccardo's code)
-  * add Tersoff potential
-  * add EAM potencial (Talad Rahman, Tapio A. Nissila)
-  * add MEAM potencial
-  * global optimization/Metadynamics
-==== Optimazlization of the code ====
-  * controll that the do-loops are written economically (ie: ratom=a*ratom;veloc=b*veloc; => do i=1,natoms; do j=1,3; ratom(j,i)=a*ratom(j,i),veloc(j,i)=a*veloc(j,i);enddo; enddo;)
-  * compare the time for 1 cycle in Fireball and Riccardo's code

Nanosurf Lab

User Tools

Site Tools

Differences

Page Tools