molecular crystals: Error in NEW_ZMATRIXCOORD

[ChrisE]

Dear All

I'm trying to learn the molecular crystal technique and I've used the benzene example with a modification; replace H with OH (just to see if I can make it work).

When I run USPEX I receive

Index exceeds matrix dimensions.

Error in NEW_ZMATRIXCOORD (line 18)
RelatedC= Coords(form,:);

Error in GetOrientation (line 50)
coords = real(NEW_ZMATRIXCOORD(Zmatrix,format));

Error in initialize_POP_STRUC_mol (line 231)
Molecules = GetOrientation(candidate, lat, numSites(:,1), Operation,
MtypeLIST);

Error in ev_alg (line 101)
initialize_POP_STRUC_mol;

I would be extremely grateful if anyone can see my mistake

Chris
 
My MOL_1 file is

H6C6O6
Number of atoms: 18
0 0 0                         6 0  0 0  1 1 1
1.63382 0.042977 0.094272     6 1  3 8  0 1 1
2.38958 -1.37571 0.403735     6 2  4 9  0 0 1
1.73699 -2.7079 -0.285838     6 3  5 10 0 0 0
0.10271 -2.7684 -0.338365     6 4  6 11 0 0 0
-0.672186 -1.35568 -0.625144  6 5  7 12 0 0 0
-0.71357 0.977572 0.386955    8 1  18 2 0 0 0
2.2838 1.1237 -0.061766       8 2  17 3 0 0 0
3.42504 -1.43726 1.13744      8 3  15 2 0 0 0
2.45886 -3.63999 -0.759309    8 4  14 3 0 0 0
-0.531577 -3.85589 -0.167049  8 5  16 4 0 0 0
-1.75036 -1.31346 -1.29631    8 6  13 1 0 0 0
-2.27642 -1.60471 -0.394265   1 12 6 1 0 0 0
2.72358 -4.10471 -0.094265    1 10 4 3 0 0 0
4.42358 -1.40471 0.661835     1 9  3 2 0 0 0
-0.476419 -4.50471 -0.594265  1 11 5 4 0 0 0
2.75383 1.41776 1.09851       1 8  2 1 0 0 0
-0.676419 1.79529 -0.194265   1 7  1 2 0 0 0

and the INPUT.txt is below. I have tried a 3x3 matrix for the ion distances but the index exceeds matrix error still occurs.

PARAMETERS EVOLUTIONARY ALGORITHM

******************************************
******************************************
*      TYPE OF RUN AND SYSTEM            *
******************************************
******************************************
USPEX : calculationMethod (USPEX, VCNEB, META)
310   : calculationType (dimension: 0-3; molecule: 0/1; varcomp: 0/1)
1     : optType (optimise by: 1=enthalpy, 2=volume, 3=hardness, 4=struc_order, 5=aver_dist, 6=mag_moment)

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% What symmetry(s) have to be satisfied by the randomly created structures
% symmetries
2-230
% endSymmetries

% numbers of specices (ions/molecules/blocks) of each type
% numSpecices
4
% EndNumSpecices
%%%%%%%%%%%%%%%%%%%%
% Here come the atomic numbers of the atoms involved
% atomType
C O H
% EndAtomType
%%%%%%%%%%%%%%%%%%%%
% valences
4 2 1
% endValences

******************************************
*               POPULATION               *
******************************************
20    : populationSize (how many individuals per generation)
20    : initialPopSize
20    : numGenerations (how many generations shall be calculated)
10    : stopCrit

******************************************
*  SURVIVAL OF THE FITTEST AND SELECTION *
******************************************
1     : reoptOld
0.6   : bestFrac

******************************************
******************************************
*          VARIATION OPERATORS           *
******************************************
******************************************
0.50  : fracGene (fraction of generation produced by heredity)
0.20  : fracRand (fraction of generation produced randomly from space groups)
0.10  : fracAtomsMut (fraction of the generation produced by softmutation)
0.20  : fracRotMut (fraction of the generation produced by rotation)
0.00  : fracPerm  (fraction of the generation produced by permutations)


****************************************
*             CONSTRAINTS              *
****************************************
% IonDistances
0.6
% EndDistances

*****************************************
*                 CELL                  *
*****************************************
% The following is what you know about the lattice. If you know the lattice
% vectors, type them in as 3x3 matrix. If not, type the estimated volume.
% For variable composition - type the estimated atomic volume for each element.
% Latticevalues (this word MUST stay here, type values below)
250
% Endvalues (this word MUST stay here)

*****************************************
*   DETAILS OF AB INITIO CALCULATIONS   *
*****************************************
% vasp (1), siesta (2), gulp (3), etc
abinitioCode (which code from CommandExecutable shall be used for calculation? )
1 1 1 1
ENDabinit

%Resolution for KPOINTS - one number per step or just one number in total)
% KresolStart
0.16 0.14 0.12 0.10
%  Kresolend

% commandExecutable
./job.sh
% EndExecutable

1     : numParallelCalcs (how many parallel calculations shall be performed)
0     : whichCluster (on which cluster are calculations performed)
0.010 : toleranceFing (tolerance for identical structures)

[Muthukumar Kaliappan]

% numSpecices
4
% EndNumSpecices
%%%%%%%%%%%%%%%%%%%%
% Here come the atomic numbers of the atoms involved
% atomType
C O H
% EndAtomType

Should be 

% numSpecices
4  X  X

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Muthukumar Kaliappan

Room 1.144
Institute for Theoretical Physics
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[Qiang Zhu]

The part of MOL_* file is currently not well documented. But you can still have a basic idea from the following link:

http://uspex.stonybrook.edu/Manual/module_4_13.htm?ms=ARA=&mw=MjQw&st=MA==&sct=MA==

H6C6O6
Number of atoms: 18
0 0 0                         6 0  0 0  1 1 1
1.63382 0.042977 0.094272     6 1  3 8  0 1 1

>The columns 5-7 are used to specify the topological relations. That is, the atom should >connect which to form the bond length, bond angle and dihedral angles. The atomic index must >be in the sequence as we define it one by one. For the first three atoms, this table must follow the rules like:

>0 0 0

>1 0 0

>1 2 0

>.....

2.38958 -1.37571 0.403735     6 2  4 9  0 0 1
1.73699 -2.7079 -0.285838     6 3  5 10 0 0 0
0.10271 -2.7684 -0.338365     6 4  6 11 0 0 0
-0.672186 -1.35568 -0.625144  6 5  7 12 0 0 0
-0.71357 0.977572 0.386955    8 1  18 2 0 0 0
2.2838 1.1237 -0.061766       8 2  17 3 0 0 0
3.42504 -1.43726 1.13744      8 3  15 2 0 0 0
2.45886 -3.63999 -0.759309    8 4  14 3 0 0 0
-0.531577 -3.85589 -0.167049  8 5  16 4 0 0 0
-1.75036 -1.31346 -1.29631    8 6  13 1 0 0 0
-2.27642 -1.60471 -0.394265   1 12 6 1 0 0 0
2.72358 -4.10471 -0.094265    1 10 4 3 0 0 0
4.42358 -1.40471 0.661835     1 9  3 2 0 0 0
-0.476419 -4.50471 -0.594265  1 11 5 4 0 0 0
2.75383 1.41776 1.09851       1 8  2 1 0 0 0
-0.676419 1.79529 -0.194265   1 7  1 2 0 0 0

% numSpecices

4
% EndNumSpecices

This tag is fine.

Best,

Qiang

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Qiang Zhu (Ph.D)
ESS 365
Department of Geosciences
Stony Brook University
NY 11794-2100

USPEX download Page: http://uspex.stonybrook.edu/

[ChrisE]

But for a molecular crystal isn't N the number of molecular crystals inside the box as in the CH4 example?

I have tried

% numSpecices
6 6 6
% EndNumSpecices
 
and it doesn't work

C

[Qiang Zhu]

% numSpecices

4
% EndNumSpecices

This tag is fine. The whole molecule should be considered as one type of specie.

Please refer to T12_molecule_VASP for details.

Qiang

[ChrisE]

For future reference I have now solved this problem. The list cannot reference an atom that has not yet appeared in the list - we cannot refer to atom 10 until after the line for atom 10. The MOL_1 file that works looks like 

C6O6H4

Number of atoms: 14

0 0 0                         6 0  0 0  1 1 1

1.63382 0.042977 0.094272     6 1  0 0  0 1 1

2.38958 -1.37571 0.403735     6 2  1 0  0 0 1

1.73699 -2.7079 -0.285838     6 3  2 1 0 0 0

0.10271 -2.7684 -0.338365     6 4  3 2 0 0 0

-0.672186 -1.35568 -0.625144  6 5  4 3 0 0 0

-0.71357 0.977572 0.386955    8 1  2 3 0 0 0

2.2838 1.1237 -0.061766       8 2  3 4 0 0 0

3.42504 -1.43726 1.13744      8 3  4 5 0 0 0

2.45886 -3.63999 -0.759309    8 4  5 6 0 0 0

-0.531577 -3.85589 -0.167049  8 5  6 5 0 0 0

-1.75036 -1.31346 -1.29631    8 6  1 2 0 0 0

2.75383 1.41776 1.09851       1 8  2 3 0 0 0

4.42358 -1.40471 0.661835     1 9  3 4 0 0 0

-0.476419 -4.50471 -0.594265  1 11 5 6 0 0 0