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Software Introduction
GULP |
GULP (General Utility Lattice Program) is designed to carry out a variety of tasks relating to 3-dimensional solids. GULP can also perform calculations on non-periodic systems, as it includes what was once a separate program called CLUSTER. This facility is useful when calculating defect energies for molecular defects. The input files contain keywords that are case-insensitive. Any lines beginning with a #, or anything that follows a # part-way through a line is treated as a comment by the program. GULP only reads the first 80 characters on a line, but lines more than 80 characters long can be continued by adding the continuation character (&) to the end of the line. The general structure of the input file is as follows. The first line is the keyword line. The keywords consist of control words, which require no further parameters and generally specify the tasks to be performed by the program. Note that GULP normally only reads the first four characters of any keyword. All subsequent lines can be given in any order and contain options requiring the specification of further information. A full list of keywords and options can be found in the GULP user manual. Structures are input in three main sections: the unit cell, the coordinates (fractional or Cartesian) and types of the atoms, and the space group symmetry. The latter is not compulsory and the symmetry group will be assumed to be P1 if not specified. The unit cell may be specified in terms of parameters or vectors. The coordinate input may contain several other pieces of information in addition to the coordinates themselves. Normally the atomic symbol is given, followed by an optional species type (usually core), then the x, y and z coordinates, and finally a number of optional parameters which can follow the z coordinate on the line. These are (in order) the charge, the site occupancy (defaults to 1), the ion radius for a breathing model (defaults to 0.0), and 3 flags to identify the geometric variables (1 = vary, 0 = fix). The latter are not needed when the variables are automatically specified using the keywords conv (constant volume calculation where the cell is held fixed) or conp (constant pressure calculation where the cell is varied). In addition to the structure, the potentials to be used in the calculation need to be specified. GULP contains many different types of potential including the Buckingham, Morse, Harmonic, Lennard-Jones and Stillinger-Weber potentials. Two-, three- and four-body potentials are all available. These potentials may be input manually using values from the literature, or else libraries of potentials are available with the program and may be specified in the input deck. Three examples are given below taken from the example suite supplied by GULP. The first shows the set up required for the optimisation of a molecular crystal, namely urea. Four different types of potential are explicitly specified in the input deck. The second example is calculation on alumina, illustrating how to assign potentials using one of the libraries available in GULP. The third example illustrates how to calculate the defect energy of a molecular defect. |
Examples |
Example 1. Optimisation of urea with explicit specification of potentials Example 2. Optimisation of alumina using a library to assign the potentials Example 3. A molecular defect calculationNote: All explanations are given in red. |
| Example 1. Optimisation of urea with explicit specification of potentials
In this example, we illustrate how to set up an input deck for the optimisation of urea at constant pressure, with calculations of the C6 dispersion energy terms and bulk lattice properties. The intramolecular potential used in this case is a Morse potential, and the intermolecular interactions are modelled using a Lennard-Jones 12-6 potential, a three-body harmonic potential and a general four-body potential. Note that the molecule facility in GULP can be used to locate molecules within the structures input based on the covalent radii of the atoms, and then the user can choose how to handle the Coulomb interactions within these molecules. In this case the molecule keyword is used to specify that any Coulomb interactions within the molecules should be excluded. |
Input |
ex1.dat
opti molecule conp prop c6 Keyword line. title Title line specification. example of a molecular crystal - urea end End of title line specification. cell Cell specification: x, y, z, alpha, beta, gamma, vectors. 5.550830 5.550830 4.695612 90.000038 89.999963 89.999803 1 1 1 1 1 1 fractional 16 Fractional coordinates for 16 atoms with charges specified below. C core 0.00000000 0.50000000 0.32600000 0.380000 C core 0.49999920 0.00000080 0.61502595 0.380000 O core 0.00000000 0.49999998 0.58816619 -0.380000 O core 0.50000040 -0.00000039 0.35285659 -0.380000 N core 0.14293176 0.64293184 0.18101006 -0.830000 N core 0.85706814 0.35706821 0.18101006 -0.830000 N core 0.64293288 0.85706713 0.76001372 -0.830000 N core 0.35706811 0.14293188 0.76001345 -0.830000 H core 0.26167656 0.76167659 0.27731462 0.415000 H core 0.73832344 0.23832347 0.27731458 0.415000 H core 0.76167757 0.73832243 0.66370978 0.415000 H core 0.23832195 0.26167805 0.66370971 0.415000 H core 0.13785881 0.63785890 0.96043229 0.415000 H core 0.86214114 0.36214121 0.96043228 0.415000 H core 0.63785790 0.86214210 -0.01940859 0.415000 H core 0.36214109 0.13785891 -0.01940832 0.415000 morse intra Morse intramolecular potential specified with cutoff at 1.6 Å. C core O core 6.288000 2.060000 1.23000 0.0000 1.600 morse intra D a ro C core N core 4.206000 2.000000 1.32000 0.0000 1.600 morse intra H core N core 3.816000 2.280000 1.02600 0.0000 1.600 lennard 12 6 inter Lennard-Jones 12-6 intermolecular potential specified with cutoff at 40 Å. C core O core 39031.570000 35.266000 0.000 40.000 lennard 12 6 inter A B C core N core 112494.667000 55.387000 0.000 40.000 lennard 12 6 inter O core O core 11833.864000 21.633000 0.000 40.000 lennard 12 6 inter N core O core 34106.919000 33.977000 0.000 40.000 lennard 12 6 inter N core N core 98301.108000 53.362000 0.000 40.000 lennard 12 6 inter C core C core 128737.614000 57.488000 0.000 40.000 three Three-body general harmonic potential specified with cutoffs for 1-2, 1-3 and 2-3 interactions. C core N core O core 5.897000 121.000000 1.600 1.600 3.000 three k2 θ cutoffs N core H core C core 3.252000 120.000000 1.400 1.600 2.600 three N core H core H core 2.862000 120.000000 1.400 1.400 2.300 three C core N core N core 8.846000 118.000000 1.600 1.600 2.800 torsion Four-body potential specified with cutoffs for 1-2, 2-3, 3-4 and 4-1 interactions. O cor C cor N cor H cor 0.260200 -2 1.40 1.40 1.30 0.00 torsion k cutoffs N cor C cor N cor H cor 0.002170 -2 1.60 1.60 1.30 0.00 torsion O cor C cor N cor N cor 0.434000 -2 1.60 1.60 3.00 0.00 Keyword line: opti = optimise the structure molecule = locate molecules and exclude Coulomb interactions within molecules conp = constant pressure calculation (cell to vary) prop = calculate bulk lattice properties (elastic constant, bulk modulus, Young's modulii, refractive index) c6 = calculate C6 dispersion energy terms Input file (gzipped) ex1.dat can be downloaded here. |
Output |
using 4 processors
********************************************************************************
* GENERAL UTILITY LATTICE PROGRAM *
* Julian Gale, Imperial College *
* Version 1.3 *
********************************************************************************
* optimise - perform optimisation run * Summary of options chosen.
* conp - constant pressure calculation *
* property - calculate properties for final geometry *
* molecule - molecule option activated, coulomb subtract within molecule *
********************************************************************************
* example of a molecular crystal - urea * Title line.
********************************************************************************
Number of CPUs = 4 Number of processors used in calculation.
Total number of configurations input = 1
********************************************************************************
* Input for Configuration = 1 *
********************************************************************************
Formula = C2O2N4H8 Formula of system.
Number of irreducible atoms/shells = 16
Total number atoms/shells = 16
Dimensionality = 3 3-dimensional solid.
Cartesian lattice vectors (Angstroms) :
5.550830 0.000000 0.000000
0.000019 5.550830 0.000000
0.000003 -0.000003 4.695612
Cell parameters (Angstroms/Degrees):
a = 5.5508 alpha = 90.0000
b = 5.5508 beta = 90.0000
c = 4.6956 gamma = 89.9998
Initial cell volume = 144.679853 Angs**3
Temperature of configuration = 0.000 K
Pressure of configuration = 0.000 GPa
Fractional coordinates of asymmetric unit :
* indicates variables to be optimised.
--------------------------------------------------------------------------------
No. Atomic x y z Charge Occupancy
Label (Frac) (Frac) (Frac) (e) (Frac)
--------------------------------------------------------------------------------
1 C c 0.000000 0.500000 0.326000 0.380000 1.000000
2 C c 0.499999 * 0.000001 * 0.615026 * 0.380000 1.000000
3 O c 0.000000 * 0.500000 * 0.588166 * -0.380000 1.000000
4 O c 0.500000 * 1.000000 * 0.352857 * -0.380000 1.000000
5 N c 0.142932 * 0.642932 * 0.181010 * -0.830000 1.000000
6 N c 0.857068 * 0.357068 * 0.181010 * -0.830000 1.000000
7 N c 0.642933 * 0.857067 * 0.760014 * -0.830000 1.000000
8 N c 0.357068 * 0.142932 * 0.760013 * -0.830000 1.000000
9 H c 0.261677 * 0.761677 * 0.277315 * 0.415000 1.000000
10 H c 0.738323 * 0.238323 * 0.277315 * 0.415000 1.000000
11 H c 0.761678 * 0.738322 * 0.663710 * 0.415000 1.000000
12 H c 0.238322 * 0.261678 * 0.663710 * 0.415000 1.000000
13 H c 0.137859 * 0.637859 * 0.960432 * 0.415000 1.000000
14 H c 0.862141 * 0.362141 * 0.960432 * 0.415000 1.000000
15 H c 0.637858 * 0.862142 * 0.980591 * 0.415000 1.000000
16 H c 0.362141 * 0.137859 * 0.980592 * 0.415000 1.000000
--------------------------------------------------------------------------------
Molecule list generated from bondlengths :
Total number of molecules = 2
--------------------------------------------------------------------------------
Molecule No./: Atoms
Periodicity :
--------------------------------------------------------------------------------
1 0 : C c 1 O c 3 N c 5 N c 6 H c 9 H c 10
: H c 13 H c 14
2 0 : C c 2 O c 4 N c 7 N c 8 H c 11 H c 12
: H c 15 H c 16
--------------------------------------------------------------------------------
********************************************************************************
* General input information *
********************************************************************************
Species output for all configurations :
--------------------------------------------------------------------------------
Species Type Atomic Atomic Charge Radii (Angs) Library
Number Mass (e) Covalent Ionic Symbol
--------------------------------------------------------------------------------
C Core 6 12.01 0.3800 0.770 0.000
O Core 8 16.00 -0.3800 0.730 0.000
N Core 7 14.01 -0.8300 0.750 0.000
H Core 1 1.01 0.4150 0.370 0.000
--------------------------------------------------------------------------------
Accuracy factor for lattice sums = 8.000
Time limit = Infinity
C6 terms to be calculated in real and reciprocal space
Intramolecular potentials : Morse potentials used.
--------------------------------------------------------------------------------
Atom Types Potential A B C D Cutoffs(Ang)
1 2 Min Max
--------------------------------------------------------------------------------
C c O c Morse 6.29 2.06 1.23 .000E+00 0.000 1.600
C c N c Morse 4.21 2.00 1.32 .000E+00 0.000 1.600
H c N c Morse 3.82 2.28 1.03 .000E+00 0.000 1.600
--------------------------------------------------------------------------------
Intermolecular potentials : Lennard-Jones 12-6 potentials used.
--------------------------------------------------------------------------------
Atom Types Potential A B C D Cutoffs(Ang)
1 2 Min Max
--------------------------------------------------------------------------------
C c O c Lennard 12 6 .3903E+05 35.27 .000E+00 .000E+00 0.000 40.000
C c N c Lennard 12 6 .1125E+06 55.39 .000E+00 .000E+00 0.000 40.000
O c O c Lennard 12 6 .1183E+05 21.63 .000E+00 .000E+00 0.000 40.000
N c O c Lennard 12 6 .3411E+05 33.98 .000E+00 .000E+00 0.000 40.000
N c N c Lennard 12 6 .9830E+05 53.36 .000E+00 .000E+00 0.000 40.000
C c C c Lennard 12 6 .1287E+06 57.49 .000E+00 .000E+00 0.000 40.000
--------------------------------------------------------------------------------
General Three-body potentials :
Harmonic form:
--------------------------------------------------------------------------------
Atom Atom Atom Force Constants Theta Cutoffs
1 2 3 (eVrad**-2/eVrad**-3/eVrad**-4) (deg) 1-2 1-3 2-3
--------------------------------------------------------------------------------
C c N c O c 5.897 0.0000 0.0000 121.000 1.60 1.60 3.00
N c H c C c 3.252 0.0000 0.0000 120.000 1.40 1.60 2.60
N c H c H c 2.862 0.0000 0.0000 120.000 1.40 1.40 2.30
C c N c N c 8.846 0.0000 0.0000 118.000 1.60 1.60 2.80
--------------------------------------------------------------------------------
General Four-body potentials :
Standard form:
--------------------------------------------------------------------------------
Atom Types Force cst Sign Phase Phi0 Cutoffs
1 2 3 4 (eV) 1-2 2-3 3-4 4-1
--------------------------------------------------------------------------------
O c C c N c H c .26020 - 2 0.00 1.40 1.40 1.30 0.00
N c C c N c H c .21700E-02 - 2 0.00 1.60 1.60 1.30 0.00
O c C c N c N c .43400 - 2 0.00 1.60 1.60 3.00 0.00
--------------------------------------------------------------------------------
********************************************************************************
* Output for configuration 1 *
********************************************************************************
Components of energy :
--------------------------------------------------------------------------------
Interatomic potentials = -58.75443265 eV
Three-body potentials = 0.02546153 eV
Four-body potentials = 0.00000000 eV
Out of plane potentials = 0.00000000 eV
Monopole - monopole (real) = 18.63335466 eV
Monopole - monopole (recip)= -20.29103531 eV
Monopole - monopole (total)= -1.65768065 eV
Dispersion (real+recip) = -1.69282021 eV
--------------------------------------------------------------------------------
Total lattice energy = -62.07947199 eV
--------------------------------------------------------------------------------
Total lattice energy = -5989.7201 kJ/(mole unit cells)
--------------------------------------------------------------------------------
Number of variables = 51
Maximum number of calculations = 1000
Maximum Hessian update interval = 10
Maximum step size = 1.0000000
Maximum parameter tolerance = 0.0000100
Maximum function tolerance = 0.0000100
Maximum gradient tolerance = 0.0000100
Symmetry not applied to optimisation
Newton-Raphson optimiser to be used
BFGS hessian update to be used
Start of bulk optimisation :
Cycle: 0 Energy: -62.079472 Gnorm: 0.000221 CPU: 4.147
** Hessian calculated **
Cycle: 1 Energy: -62.079474 Gnorm: 0.000001 CPU: 4.173
**** Optimisation achieved **** Structure optimised.
Final energy = -62.07947405 Final optimised energy in eV.
Final Gnorm = 0.00000080
Components of energy :
--------------------------------------------------------------------------------
Interatomic potentials = -58.75337801 eV
Three-body potentials = 0.02538993 eV
Four-body potentials = 0.00000000 eV
Out of plane potentials = 0.00000000 eV
Monopole - monopole (real) = 18.63572680 eV
Monopole - monopole (recip)= -20.29335002 eV
Monopole - monopole (total)= -1.65762322 eV
Dispersion (real+recip) = -1.69386274 eV
--------------------------------------------------------------------------------
Total lattice energy = -62.07947405 eV
--------------------------------------------------------------------------------
Total lattice energy = -5989.7203 kJ/(mole unit cells)
--------------------------------------------------------------------------------
Final fractional coordinates of atoms :
--------------------------------------------------------------------------------
No. Atomic x y z Radius
Label (Frac) (Frac) (Frac) (Angs)
--------------------------------------------------------------------------------
1 C c 0.000000 0.500000 0.326000 0.000000
2 C c 0.500000 0.000000 0.615274 0.000000
3 O c 0.000000 0.500000 0.588128 0.000000
4 O c 0.500000 0.000000 0.353147 0.000000
5 N c 0.142970 0.642970 0.181040 0.000000
6 N c 0.857030 0.357030 0.181040 0.000000
7 N c 0.642970 0.857030 0.760235 0.000000
8 N c 0.357030 0.142970 0.760235 0.000000
9 H c 0.261741 0.761741 0.277351 0.000000
10 H c 0.738259 0.238259 0.277351 0.000000
11 H c 0.761741 0.738259 0.663924 0.000000
12 H c 0.238259 0.261741 0.663924 0.000000
13 H c 0.137914 0.637914 0.960498 0.000000
14 H c 0.862086 0.362086 0.960498 0.000000
15 H c 0.637914 0.862086 0.980777 0.000000
16 H c 0.362086 0.137914 0.980777 0.000000
--------------------------------------------------------------------------------
Final cell parameters and derivatives : New cell parameters.
--------------------------------------------------------------------------------
a 5.549398 Angstrom dE/de1(xx) -0.000014 eV/strain
b 5.549398 Angstrom dE/de2(yy) -0.000014 eV/strain
c 4.696336 Angstrom dE/de3(zz) -0.000027 eV/strain
alpha 90.000000 Degrees dE/de4(yz) 0.000000 eV/strain
beta 90.000000 Degrees dE/de5(xz) 0.000000 eV/strain
gamma 90.000000 Degrees dE/de6(xy) 0.000000 eV/strain
--------------------------------------------------------------------------------
Primitive cell volume = 144.627480 Angs**3
Density of cell = 1.379408 g/cm**3
Non-primitive cell volume = 144.627480 Angs**3
Final internal derivatives :
--------------------------------------------------------------------------------
No. Atomic x y z Radius
Label (eV) (eV) (eV) (eV/Angs)
--------------------------------------------------------------------------------
1 C c 0.000000 0.000000 0.000000 0.000000
2 C c -0.000002 0.000002 0.000007 0.000000
3 O c 0.000000 0.000000 0.000005 0.000000
4 O c 0.000000 0.000000 -0.000004 0.000000
5 N c -0.000002 -0.000002 -0.000004 0.000000
6 N c 0.000002 0.000002 -0.000004 0.000000
7 N c -0.000001 0.000001 0.000004 0.000000
8 N c 0.000004 -0.000004 0.000004 0.000000
9 H c -0.000005 -0.000005 -0.000004 0.000000
10 H c 0.000005 0.000005 -0.000004 0.000000
11 H c -0.000005 0.000005 0.000004 0.000000
12 H c 0.000004 -0.000004 0.000004 0.000000
13 H c -0.000001 -0.000001 0.000004 0.000000
14 H c 0.000001 0.000001 0.000004 0.000000
15 H c -0.000002 0.000002 -0.000004 0.000000
16 H c 0.000001 -0.000001 -0.000004 0.000000
--------------------------------------------------------------------------------
Bulk properties calculated.
Elastic Constant Matrix: (Units=10**11 Dyne/cm**2= 10 GPa)
-------------------------------------------------------------------------------
Indices 1 2 3 4 5 6
-------------------------------------------------------------------------------
1 1.70988 1.70765 1.15882 0.00000 0.00000 0.00001
2 1.70765 1.70988 1.15882 0.00000 0.00000 -0.00001
3 1.15882 1.15882 6.87017 0.00000 0.00000 0.00000
4 0.00000 0.00000 0.00000 0.51299 0.00000 0.00000
5 0.00000 0.00000 0.00000 0.00000 0.51299 0.00000
6 0.00001 -0.00001 0.00000 0.00000 0.00000 2.21802
-------------------------------------------------------------------------------
Bulk Modulus (GPa) = 16.60462
Stress axis : x y z
-------------------------------------------------------------------------------
Youngs Modulii (GPa) = 0.04438 0.04438 60.84312
-------------------------------------------------------------------------------
Poissons Ratio (x) = 0.99853 0.33908
Poissons Ratio (y) = 0.99853 0.33908
Poissons Ratio (z) = 0.00025 0.00025
-------------------------------------------------------------------------------
Piezoelectric Stress Matrix: (Units= C/m**2)
-------------------------------------------------------------------------------
Indices 1 2 3 4 5 6
-------------------------------------------------------------------------------
x 0.00000 0.00000 0.00000 1.49181 0.00001 0.00000
y 0.00000 0.00000 0.00000 -0.00001 1.49181 0.00000
z 0.00000 0.00000 0.00000 0.00000 0.00000 0.19244
-------------------------------------------------------------------------------
Piezoelectric Strain Matrix: (Units=10**-7 C/dyne)
-------------------------------------------------------------------------------
Indices 1 2 3 4 5 6
-------------------------------------------------------------------------------
x 0.00000 0.00000 0.00000 2.90804 0.00001 0.00000
y 0.00000 0.00000 0.00000 -0.00001 2.90804 0.00000
z 0.00000 0.00000 0.00000 0.00000 0.00000 0.08676
-------------------------------------------------------------------------------
Static dielectric constant tensor :
-------------------------------------------------------------------------------
x y z
-------------------------------------------------------------------------------
x 1.78210 0.00000 0.00000
y 0.00000 1.78210 0.00000
z 0.00000 0.00000 1.19911
--------------------------------------------------------------------------------
Static refractive indices :
-------------------------------------------------------------------------------
1 = 1.09504 2 = 1.33495 3 = 1.33495
-------------------------------------------------------------------------------
Time to end of optimisation = 4.2066 seconds
Timing analysis for Gulp : CPU time used in calculation.
--------------------------------------------------------------------------------
Task / Subroutine Time (Seconds)
--------------------------------------------------------------------------------
Calculation of reciprocal space energy and derivatives 0.0319
Calculation of real space energy and derivatives 0.0764
Calculation of three-body energy and derivatives 0.0034
Calculation of four-body energy and derivatives 0.0022
Calculation of properties 0.0017
Calculation of hessian 0.0001
Matrix inversion 0.0009
Global summation overhead 0.0043
--------------------------------------------------------------------------------
Total CPU time 4.2068
--------------------------------------------------------------------------------
Output file (gzipped) ex1.out can be downloaded here. |
| Example 2. Optimisation of alumina using a library to assign the potentials
This is an example of an optimisation of alumina at constant pressure, with a bulk lattice properties calculation. The potentials in this case are taken from one of the libraries that are available with GULP. GULP currently comes with two library files, one for studying zeolites and aluminophosphates (catlow.lib) and one for studying metal oxides (bush.lib). The latter is used in this example. The options in the input file also request that a dumpfile (ex2.res) be written for restarts. |
Input |
ex2.dat
# # BUSH -library of potentials for GULP # # from T.S.Bush, J.D.Gale, C.R.A.Catlow and P.D. Battle # J. Mater Chem., 4, 831-837 (1994) # species Li core 1.000 Na core 1.000 K core 1.000 Mg core 1.580 Mg shel 0.420 Ca core 0.719 Ca shel 1.281 Sr core 0.169 Sr shel 1.831 Ba core 0.169 Ba shel 1.831 Fe core 1.971 Fe shel 1.029 Ti core 2.332 Ti shel 1.668 Al core 0.043 Al shel 2.957 Ga core 3.000 Y core 3.000 La core 5.149 La shel -2.149 Pr core 1.678 Pr shel 1.322 Nd core 1.678 Nd shel 1.322 Gd core -0.973 Gd shel 3.973 Eu core -0.991 Eu shel 3.991 Tb core -0.972 Tb shel 3.972 Yb core -0.278 Yb shel 3.278 O core 0.513 O shel -2.513 buckingham Li core O shel 426.480 0.3000 0.00 0.0 10.0 Na core O shel 1271.504 0.3000 0.00 0.0 10.0 K core O shel 3587.570 0.3000 0.00 0.0 10.0 Mg shel O shel 2457.243 0.2610 0.00 0.0 10.0 Ca shel O shel 2272.741 0.2986 0.00 0.0 10.0 Sr shel O shel 1956.702 0.3252 0.00 0.0 10.0 Ba shel O shel 4818.416 0.3067 0.00 0.0 10.0 Fe shel O shel 3219.335 0.2641 0.00 0.0 10.0 Ti shel O shel 2088.107 0.2888 0.00 0.0 10.0 Al shel O shel 2409.505 0.2649 0.00 0.0 10.0 Ga core O shel 2339.776 0.2742 0.00 0.0 10.0 Y core O shel 1519.279 0.3291 0.00 0.0 10.0 La shel O shel 5436.827 0.2939 0.00 0.0 10.0 Pr shel O shel 13431.118 0.2557 0.00 0.0 10.0 Nd shel O shel 13084.217 0.2550 0.00 0.0 10.0 Gd shel O shel 866.339 0.3770 0.00 0.0 10.0 Eu shel O shel 847.868 0.3791 0.00 0.0 10.0 Tb shel O shel 845.137 0.3750 0.00 0.0 10.0 Yb shel O shel 991.029 0.3515 0.00 0.0 10.0 O shel O shel 25.410 0.6937 32.32 0.0 12.0 spring Mg 349.95 Ca 34.05 Sr 21.53 Ba 34.05 Fe 179.58 Ti 253.60 Al 403.98 La 173.90 Pr 302.36 Nd 302.35 Gd 299.96 Eu 304.92 Tb 299.98 Yb 308.91 O 20.53 Input file (gzipped) ex2.dat can be downloaded here. Input file (gzipped) bush.lib can be downloaded here. |
Output |
using 4 processors
********************************************************************************
* GENERAL UTILITY LATTICE PROGRAM *
* Julian Gale, Imperial College *
* Version 1.3 *
********************************************************************************
* optimise - perform optimisation run *
* conp - constant pressure calculation *
* property - calculate properties for final geometry *
********************************************************************************
* alumina - example of how to use a library to assign *
* the potentials *
********************************************************************************
Number of CPUs = 4
Total number of configurations input = 1
********************************************************************************
* Input for Configuration = 1 *
********************************************************************************
Formula = Al4O6
Number of irreducible atoms/shells = 4
Total number atoms/shells = 20
Dimensionality = 3
Symmetry :
Crystal family : Hexagonal
Crystal class (Groth - 1921) : Ditrigonal Scalenohedral
Space group (centrosymmetric) : R -3 C
Space group 167.
Patterson group : R -3 m
Cartesian lattice vectors (Angstroms) :
2.380100 1.374151 4.331100
-2.380100 1.374151 4.331100
0.000000 -2.748303 4.331100
Primitive cell parameters : Full cell parameters :
a = 5.1295 alpha = 55.2915 a = 4.7602 alpha = 90.0000
b = 5.1295 beta = 55.2915 b = 4.7602 beta = 90.0000
c = 5.1295 gamma = 55.2915 c = 12.9933 gamma = 120.0000
Initial volumes (Angstroms**3):
Primitive cell = 84.992234 Full cell = 254.976701
Temperature of configuration = 0.000 K
Pressure of configuration = 0.000 GPa
Fractional coordinates of asymmetric unit :
--------------------------------------------------------------------------------
No. Atomic x y z Charge Occupancy
Label (Frac) (Frac) (Frac) (e) (Frac)
--------------------------------------------------------------------------------
1 Al c 0.000000 0.000000 0.352160 * 0.043000 1.000000
2 O c 0.306240 * 0.000000 0.250000 0.513000 1.000000
3 Al s 0.000000 0.000000 0.352160 * 2.957000 1.000000
4 O s 0.306240 * 0.000000 0.250000 -2.513000 1.000000
--------------------------------------------------------------------------------
Constraints :
--------------------------------------------------------------------------------
Constraint no. Unconstrained Constrained Coefficient Offset
Variable Variable
--------------------------------------------------------------------------------
1 Strain 1 Strain 2 1.00000 0.0000
--------------------------------------------------------------------------------
********************************************************************************
* General input information *
********************************************************************************
Species output for all configurations :
--------------------------------------------------------------------------------
Species Type Atomic Atomic Charge Radii (Angs) Library
Number Mass (e) Covalent Ionic Symbol
--------------------------------------------------------------------------------
Al Core 13 26.98 0.0430 1.350 0.000
O Core 8 16.00 0.5130 0.730 0.000
Al Shell 13 0.00 2.9570 1.350 0.000
O Shell 8 0.00 -2.5130 0.730 0.000
--------------------------------------------------------------------------------
Accuracy factor for lattice sums = 8.000
Time limit = Infinity
General interatomic potentials : Intermolecular potentials(including cutoffs) read from library file as specified.
--------------------------------------------------------------------------------
Atom Types Potential A B C D Cutoffs(Ang)
1 2 Min Max
--------------------------------------------------------------------------------
O s Al s Buckingham 0.241E+04 0.265 .000E+00 .000E+00 0.000 10.000
O s O s Buckingham 25.4 0.694 32.3 .000E+00 0.000 12.000
Al c Al s Spring (c-s) 404. 0.000E+00 .000E+00 .000E+00 0.000 0.600
O c O s Spring (c-s) 20.5 0.000E+00 .000E+00 .000E+00 0.000 0.600
--------------------------------------------------------------------------------
********************************************************************************
* Output for configuration 1 *
********************************************************************************
Components of energy :
--------------------------------------------------------------------------------
Interatomic potentials = 63.08517294 eV
Monopole - monopole (real) = -67.28514814 eV
Monopole - monopole (recip)= -310.49814544 eV
Monopole - monopole (total)= -377.78329358 eV
--------------------------------------------------------------------------------
Total lattice energy :
Primitive unit cell = -314.69812064 eV
Non-primitive unit cell = -944.09436191 eV
--------------------------------------------------------------------------------
Total lattice energy (in kJmol-1):
Primitive unit cell = -30363.5580 kJ/(mole unit cells)
Non-primitive unit cell = -91090.6741 kJ/(mole unit cells)
--------------------------------------------------------------------------------
Number of variables = 6
Maximum number of calculations = 1000
Maximum Hessian update interval = 10
Maximum step size = 1.0000000
Maximum parameter tolerance = 0.0000100
Maximum function tolerance = 0.0000100
Maximum gradient tolerance = 0.0000100
Symmetry constrained optimisation
Symmetry used for second derivatives
Newton-Raphson optimiser to be used
BFGS hessian update to be used
Start of bulk optimisation :
Cycle: 0 Energy: -314.698121 Gnorm: 19.420599 CPU: 2.792
** Hessian calculated **
Cycle: 1 Energy: -315.172729 Gnorm: 0.362469 CPU: 9.929
Cycle: 2 Energy: -315.173275 Gnorm: 0.058523 CPU: 17.642
Cycle: 3 Energy: -315.173283 Gnorm: 0.002440 CPU: 24.622
**** Optimisation achieved **** Optimised.
Final energy = -315.17328167 Final optimised energy.
Final Gnorm = 0.00244024
Components of energy :
--------------------------------------------------------------------------------
Interatomic potentials = 59.49016556 eV
Monopole - monopole (real) = 10.85686336 eV
Monopole - monopole (recip)= -385.52031059 eV
Monopole - monopole (total)= -374.66344723 eV
--------------------------------------------------------------------------------
Total lattice energy :
Primitive unit cell = -315.17328167 eV
Non-primitive unit cell = -945.51984501 eV
--------------------------------------------------------------------------------
Total lattice energy (in kJmol-1):
Primitive unit cell = -30409.4038 kJ/(mole unit cells)
Non-primitive unit cell = -91228.2114 kJ/(mole unit cells)
--------------------------------------------------------------------------------
Final asymmetric unit coordinates :
--------------------------------------------------------------------------------
No. Atomic x y z Radius
Label (Frac) (Frac) (Frac) (Angs)
--------------------------------------------------------------------------------
1 Al c 0.000000 0.000000 0.356233 0.000000
2 O c 0.295772 0.000000 0.250000 0.000000
3 Al s 0.000000 0.000000 0.356234 0.000000
4 O s 0.297425 0.000000 0.250000 0.000000
--------------------------------------------------------------------------------
Final cell parameters and derivatives :
Optimised cell parameters.
--------------------------------------------------------------------------------
a 5.153255 Angstrom dE/de1(xx) 0.004037 eV/strain
b 5.153255 Angstrom dE/de2(yy) 0.000000 eV/strain
c 5.153255 Angstrom dE/de3(zz) 0.002984 eV/strain
alpha 55.766626 Degrees dE/de4(yz) 0.000000 eV/strain
beta 55.766626 Degrees dE/de5(xz) 0.000000 eV/strain
gamma 55.766626 Degrees dE/de6(xy) 0.000000 eV/strain
--------------------------------------------------------------------------------
Primitive cell volume = 87.267201 Angs**3
Density of cell = 3.880295 g/cm**3
Non-primitive lattice parameters :
a = 4.820070 b = 4.820070 c = 13.011728
alpha= 90.000000 beta= 90.000000 gamma= 120.000000
Non-primitive cell volume = 261.801603 Angs**3
Final internal derivatives :
--------------------------------------------------------------------------------
No. Atomic x y z Radius
Label (eV) (eV) (eV) (eV/Angs)
--------------------------------------------------------------------------------
1 Al c 0.000000 0.000000 -0.000662 0.000000
2 O c 0.001434 0.000000 0.000000 0.000000
3 Al s 0.000000 0.000000 0.011031 0.000000
4 O s -0.008062 0.000000 0.000000 0.000000
--------------------------------------------------------------------------------
Bulk properties calculated.
Elastic Constant Matrix: (Units=10**11 Dyne/cm**2= 10 GPa)
-------------------------------------------------------------------------------
Indices 1 2 3 4 5 6
-------------------------------------------------------------------------------
1 60.74881 32.29358 18.23128 4.45895 0.00000 0.00000
2 32.29358 60.74881 18.23128 -4.45895 0.00000 0.00000
3 18.23128 18.23128 60.63402 0.00000 0.00000 0.00000
4 4.45895 -4.45895 0.00000 9.56203 0.00000 0.00000
5 0.00000 0.00000 0.00000 0.00000 9.56203 4.45895
6 0.00000 0.00000 0.00000 0.00000 4.45895 14.22762
-------------------------------------------------------------------------------
Bulk Modulus (GPa) = 352.00087
Stress axis : x y z
-------------------------------------------------------------------------------
Youngs Modulii (GPa) = 374.94387 374.94387 534.89326
-------------------------------------------------------------------------------
Poissons Ratio (x) = 0.54319 0.19595
Poissons Ratio (y) = 0.54319 0.19595
Poissons Ratio (z) = 0.13735 0.13735
-------------------------------------------------------------------------------
Piezoelectric Stress Matrix: (Units= C/m**2)
-------------------------------------------------------------------------------
Indices 1 2 3 4 5 6
-------------------------------------------------------------------------------
x 0.00002 -0.00002 0.00000 0.00001 0.00001 0.00000
y 0.00000 0.00000 0.00000 0.00001 -0.00001 -0.00002
z 0.00002 0.00002 0.00002 0.00000 0.00000 0.00000
-------------------------------------------------------------------------------
Piezoelectric Strain Matrix: (Units=10**-7 C/dyne)
-------------------------------------------------------------------------------
Indices 1 2 3 4 5 6
-------------------------------------------------------------------------------
x 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
y 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
z 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
-------------------------------------------------------------------------------
Static dielectric constant tensor :
-------------------------------------------------------------------------------
x y z
-------------------------------------------------------------------------------
x 11.29381 0.00000 0.00000
y 0.00000 11.29381 0.00000
z 0.00000 0.00000 16.36593
--------------------------------------------------------------------------------
High frequency dielectric constant tensor :
-------------------------------------------------------------------------------
x y z
-------------------------------------------------------------------------------
x 5.63017 0.00000 0.00000
y 0.00000 5.63017 0.00000
z 0.00000 0.00000 6.08940
-------------------------------------------------------------------------------
Static refractive indices :
-------------------------------------------------------------------------------
1 = 3.36063 2 = 3.36063 3 = 4.04548
-------------------------------------------------------------------------------
High frequency refractive indices :
-------------------------------------------------------------------------------
1 = 2.37280 2 = 2.37280 3 = 2.46767
-------------------------------------------------------------------------------
Time to end of optimisation = 24.6493 seconds
Timing analysis for Gulp :
CPU time used in calculation.
--------------------------------------------------------------------------------
Task / Subroutine Time (Seconds)
--------------------------------------------------------------------------------
Calculation of reciprocal space energy and derivatives 0.0041
Calculation of reciprocal space energy using symmetry 6.0958
Calculation of real space energy and derivatives 0.0176
Calculation of real space energy using symmetry 0.0364
Calculation of properties 0.0047
Matrix inversion 0.0012
Calculation of transformation matrix 0.0003
Symmetry generation of equivalent positions 0.0018
Global summation overhead 22.1465
--------------------------------------------------------------------------------
Total CPU time 24.6495
--------------------------------------------------------------------------------
Dump file written as ex2.res Dumpfile to be written as ex2.res.
# Restart file written. # Keywords: # opti prop conp # # Options: # title alumina - example of how to use a library to assign the potentials end cell 4.820070 4.820070 13.011728 90.000000 90.000000 120.000000 fractional 4 Al core 0.0000000 0.0000000 0.3562330 0.04300000 1.00000 0.00000 O core 0.2957716 0.0000000 0.2500000 0.51300000 1.00000 0.00000 Al shel 0.0000000 0.0000000 0.3562343 2.95699999 1.00000 0.00000 O shel 0.2974250 0.0000000 0.2500000 -2.5129999 1.00000 0.00000 space 167 species 4 Al core 0.043000 O core 0.513000 Al shel 2.957000 O shel -2.513000 buck O shel Al shel 2409.5050 0.264900 .00000E+00 0.000 10.000 buck O shel O shel 25.410000 0.693700 32.320 0.000 12.000 spring Al 403.98000 spring O 20.530000 dump ex2.res Output file (gzipped) ex2.out can be downloaded here. Output file (gzipped) ex2.res can be downloaded here. |