MIT 3.320 Atomistic Modeling of Materials Spring 2005 Lab 1: Handout GULP: an Empirical energy code We will be using the GULP code as our energy code. GULP is a program for performing a variety of types of simulations on 3D periodic solids, gas phase clusters, and defects in a bulk material. Further information (including online manual) can be found at the GULP website. http://gulp.curtin.edu.au GULP is free for academics There are many other potentials codes one can use. These include: Cerius2 (commercial). Includes Lennard Jones, Embedded atom, visualization, and much more. Steve Plimpton’s codes (includes Lennard-Jones and Embedded Atom method ) VEGA (various force fields for molecular systems) http://users.unimi.it/~ddl/vega/index.htm Page 1 of 91 MIT 3.320 Atomistic Modeling of Materials Spring 2005 This is a tutorial on how to get energies and lattice constants using GULP. This will walk you through problem 1a of the homework. This will also show you parts of problem 2. Problem 1 Read over problem 1 of the homework. To view the gulp1a.in file type hpcbeo2$ less gulp1a.in You can scroll through the file by typing space (to go forward), b (to go backwards) or q (to quit). The file gulp1a.in contains a face-centered cubic structure, which has 4 atoms per unit cell. The file will look something like this: opti dist comp conp 2 cell 3 3.0000000 3.0000000 3.0000000 90 90 90 4 fractional 5 Au 0.0000000 0.0000000 0.0000000 6 Au 0.0000000 0.5000000 0.5000000 7 Au 0.5000000 0.0000000 0.5000000 8 Au 0.5000000 0.5000000 0.0000000 9 lennard 12 6 10 Au core Au core 214180.2000 625.482 40.000 0 0 Line numbers are added for reference. Line 1: “opti” means to optimize the structure (relax). The “opti” flag will calculate the energy of a structure, then change the structure (depending on resulting forces and stresses) and recalculate the energy of the structure. This is repeated until equilibrium is reached. opti can be replaced by “single” which means to do a single-point calculation. That is, calculate the energy of the structure, but don’t relax. Page 2 of 9MIT 3.320 Atomistic Modeling of Materials Spring 2005 You will not change the other options, but here is what they mean. dist and comp give comparisons of lattice constants and neighbor distances before and after relaxation. conp means a constant pressure simulation Line 2,3: cell is a keyword that tells the program that you will be entering the cell in terms of a, b, c, alpha, beta, gamma (as opposed to Cartesian lattice vectors). Don’t forget to type the numbers on a new line after cell. In this case, we have input a=b=c=3.0 and ===90 as a starting configuration. All units are Angstroms. Lines 4-8 fractional is a keyword that tells the program you will be entering the atoms in fractional coordinates. Don’t forget to type the actual numbers on a new line after fractional. The format is (atom name) (x pos) (y pos) (z pos) Au 0.5000000 0.5000000 0.0000000 etc… In this case, we have input the FCC gold structure. Lines 9-10 Line 9 specifies we will be using the Lennard-Jones potential with the 12-6 exponents (don’t forget to type the actual numbers on a new line. That is the potential form is: U r = A − B 612 r r The format of the Lennard-Jones line is: (type 1) (type 2) (A) (B) (potential start) (potential cutoff) Au core Au core 214180.2 625.482 0.000 40.000 The last two ‘0’s are flags, and you can ignore them. Don’t worry about the words “core”, they are just labels. This is a potential between two Au atoms. To run the program type hpcbeo2$ gulp<(input file)>(output file) In this case, Page 3 of 9-------------------------------------------------MIT 3.320 Atomistic Modeling of Materials Spring 2005 hpcbeo2$ gulp<gulp1a.in>gulp1a.out Use “less” to read the output file (less gulp1a.out). Scroll through the file by typing space to go forward or ‘b’ to go backwards. Look for something that says Final energy = (number here) Or else the LAST occurence of Total lattice energy = (number here) There may be two occurrences of “Total lattice energy =” - there will be two if you have set “opti” in the input, one if you have set “single” This will give you your energy. To find the lattice constants after relaxation, look for something near the end of the file that looks like: Final cell parameters and derivatives : a (number here) Angstrom dE/de1(xx) -0.0007 eV/strain b (number here) Angstrom dE/de2(yy) -0.0005 eV/strain c (number here) Angstrom dE/de3(zz) -0.0005 eV/strain alpha 90.000000 Degrees dE/de4(yz) 0.0000 eV/strain beta 90.000000 Degrees dE/de5(xz) 0.0000 eV/strain gamma 90.000000 Degrees dE/de6(xy) 0.0000 eV/strain Record the value for a0 (remember a0=a=b=c for a cubic system). Don’t worry if the “strain” values are different in your calculation and this example. Problem 1b. The procedure is the same. However, instead of using “gulp1a.in” you will be using “gulp1b.in”. Make sure to copy the gulp1b.in file into your directory. Page 4 of 9MIT 3.320 Atomistic Modeling of Materials Spring 2005 Problem 2. Read over problem 2 on the homework. You will need the gulp.wrap.cu.lj and gulp.wrap.cu.eam files. For example To build the supercell, which you will need to calculate vacancy formation energies and surface energies, you will use the program buildcell The way this program works is this: buildcell will read a file gulp.wrap It will build the cell in cubic directions, according to dimensions that you specify. It is specific to fcc structures. The format of gulp.wrap is: 1 lattice constant and atomic symbol 2…N (anything you want to appear in the gulp.in file besides fractional coordinates) For example: 4.0800 Au opti dist comp conp lennard 12 6 Au core Au core 214180.2000 625.482 0.000 40.000 0 0 This file specifies a Lennard Jones potential with lattice constant of 4.0800. The program buildcell is specific to the face centered cubic structure. Thus, it knows where to put the atoms correctly. To run this program First, create the appropriate gulp.wrap file, depending on which potential you will use. These have (mostly) been made for you. If you are doing problem 2A, type (in your 3.320/LAB1/PROBLEM2 directory) hpcbeo2$ cp gulp.wrap.au.lj gulp.wrap and if you are doing problem 2B, type Page 5 of 9MIT 3.320 Atomistic Modeling of Materials Spring 2005 hpcbeo2$ cp