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#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=4
#SBATCH --time=01:00:00
#SBATCH --mem=8G
#SBATCH --partition=regular
#SBATCH --output=cube_tension-%j.out
#SBATCH --error=cube_tension-%j.stderr


#pwd
#module purge
module load MATLAB/2022b-r5
module load COMSOL/6.0

# Start the COMSOL server, usually on port 2036, if it is available, otherwise it will generate an error
comsol mphserver -np ${SLURM_CPUS_PER_TASK} -port 2036 -silent -tmpdir $TMPDIR &

# Run a MATLAB script called "test.m" which uses some COMSOL functions
matlab -nodisplay -r cube_tension

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Opening log file:  /home1/p123456/java.log.57261

                            < M A T L A B (R) >
                  Copyright 1984-2022 The MathWorks, Inc.
            R2022b Update 5 (9.13.0.2193358) 64-bit (glnxa64)
                            February 10, 2023

Warning: X does not support locale en_US.UTF-8

To get started, type doc.
For product information, visit www.mathworks.com.


MATLAB is now connected to a COMSOL Multiphysics Server at localhost:2036

Run the commands below to access the COMSOL ModelUtil commands:
import com.comsol.model.util.*
Saving model: /home1/p123456/projects/cube_tension/cube_tension.mph (Model)
>> 
###############################################################################
Hábrók Cluster
Job 15571370 for user p123456
Finished at: Tue Nov 23 15:58:08 CET 2021

Job details:
============

Job ID                         : 15571370
Name                           : script.sh
User                           : p123456
Partition                      : regularshort
Nodes                          : node4
Number of Nodes                : 1
Cores                          : 4
Number of Tasks                : 1
State                          : COMPLETED  
Submit                         : 2021-11-23T15:57:13
Start                          : 2021-11-23T15:57:14
End                            : 2021-11-23T15:58:04
Reserved walltime              : 01:00:00
Used walltime                  : 00:00:50
Used CPU time                  : 00:01:53 (Efficiency: 56.69%)
% User (Computation)           : 87.71%
% System (I/O)                 : 12.29%
Total memory reserved          : 8G
Maximum memory used            : 2.00G

Acknowledgements:
=================

Please see this page for information about acknowledging Hábrók in your publications:

https://wiki.hpc.rug.nl/habrok/introduction/scientific_output

################################################################################

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Picked up _JAVA_OPTIONS: -Xmx2048m
{Error using cube_tension
Java exception occurred:
Exception:
  com.comsol.util.exceptions.LicenseException: Could not obtain license
    for#CAD Import Module
Messages:
  Error while building 'Block 1' in 'Geometry 1':

  Could not obtain license for CAD Import Module.

  License error: -4.
Licensed number of users already reached.

.
.
.

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% Add the COMSOL MATLAB LiveLink Interface (MLI) path - required for all COMSOL API functions
addpath('/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/generic/software/COMSOL/6.0/mli');

% Start the COMSOL server on port 2036
mphstart(2036);

%
% Cube_tension.m -----------------------------------------------------------

import com.comsol.model.*
import com.comsol.model.util.*

model = ModelUtil.create('Model');

model.param.set('F_z', '10000[N]');
model.param.set('F_x', '0[N]');
model.param.set('A', '0.01[m^2]');
model.param.set('L_0', '0.1[m]');
model.param.set('E', '200e9[Pa]');

model.component.create('comp1', true);

model.component('comp1').geom.create('geom1', 3);

model.result.table.create('tbl1', 'Table');
model.result.table.create('tbl2', 'Table');

model.component('comp1').mesh.create('mesh1');

model.component('comp1').geom('geom1').geomRep('comsol');
model.component('comp1').geom('geom1').create('blk1', 'Block');
model.component('comp1').geom('geom1').feature('blk1').set('size', [0.1 0.1 0.1]);
model.component('comp1').geom('geom1').run;

model.component('comp1').material.create('mat2', 'Common');
model.component('comp1').material('mat2').propertyGroup.create('Enu', 'Young''s modulus and Poisson''s ratio');

model.component('comp1').physics.create('solid', 'SolidMechanics', 'geom1');
model.component('comp1').physics('solid').create('fix1', 'Fixed', 2);
model.component('comp1').physics('solid').feature('fix1').selection.set([3]);
model.component('comp1').physics('solid').create('pc1', 'PeriodicCondition', 2);
model.component('comp1').physics('solid').feature('pc1').selection.set([1 6]);
model.component('comp1').physics('solid').create('pc2', 'PeriodicCondition', 2);
model.component('comp1').physics('solid').feature('pc2').selection.set([2 5]);
model.component('comp1').physics('solid').create('bndl1', 'BoundaryLoad', 2);
model.component('comp1').physics('solid').feature('bndl1').selection.set([4]);

model.component('comp1').mesh('mesh1').create('auto_f1', 'FreeTet');

model.result.table('tbl1').comments('Poisson Ratio');
model.result.table('tbl2').comments('Young''s Modulus');

model.component('comp1').material('mat2').label('Iron');
model.component('comp1').material('mat2').set('family', 'iron');
model.component('comp1').material('mat2').propertyGroup('def').set('relpermeability', {'4000' '0' '0' '0' '4000' '0' '0' '0' '4000'});
model.component('comp1').material('mat2').propertyGroup('def').descr('relpermeability_symmetry', '');
model.component('comp1').material('mat2').propertyGroup('def').set('electricconductivity', {'1.12e7[S/m]' '0' '0' '0' '1.12e7[S/m]' '0' '0' '0' '1.12e7[S/m]'});
model.component('comp1').material('mat2').propertyGroup('def').descr('electricconductivity_symmetry', '');
model.component('comp1').material('mat2').propertyGroup('def').set('thermalexpansioncoefficient', {'12.2e-6[1/K]' '0' '0' '0' '12.2e-6[1/K]' '0' '0' '0' '12.2e-6[1/K]'});
model.component('comp1').material('mat2').propertyGroup('def').descr('thermalexpansioncoefficient_symmetry', '');
model.component('comp1').material('mat2').propertyGroup('def').set('heatcapacity', '440[J/(kg*K)]');
model.component('comp1').material('mat2').propertyGroup('def').descr('heatcapacity_symmetry', '');
model.component('comp1').material('mat2').propertyGroup('def').set('relpermittivity', {'1' '0' '0' '0' '1' '0' '0' '0' '1'});
model.component('comp1').material('mat2').propertyGroup('def').descr('relpermittivity_symmetry', '');
model.component('comp1').material('mat2').propertyGroup('def').set('density', '7870[kg/m^3]');
model.component('comp1').material('mat2').propertyGroup('def').descr('density_symmetry', '');
model.component('comp1').material('mat2').propertyGroup('def').set('thermalconductivity', {'76.2[W/(m*K)]' '0' '0' '0' '76.2[W/(m*K)]' '0' '0' '0' '76.2[W/(m*K)]'});
model.component('comp1').material('mat2').propertyGroup('def').descr('thermalconductivity_symmetry', '');
model.component('comp1').material('mat2').propertyGroup('Enu').set('youngsmodulus', '200e9[Pa]');
model.component('comp1').material('mat2').propertyGroup('Enu').descr('youngsmodulus_symmetry', '');
model.component('comp1').material('mat2').propertyGroup('Enu').set('poissonsratio', '0.29');
model.component('comp1').material('mat2').propertyGroup('Enu').descr('poissonsratio_symmetry', '');

model.component('comp1').physics('solid').feature('pc1').set('PeriodicType', 'userdef');
model.component('comp1').physics('solid').feature('pc1').set('PeriodicIn', [1; 0; 0]);
model.component('comp1').physics('solid').feature('pc1').set('ComponentPeriodicType', {'AntiPeriodicity'; 'Continuity'; 'Continuity'});
model.component('comp1').physics('solid').feature('pc2').set('PeriodicType', 'userdef');
model.component('comp1').physics('solid').feature('pc2').set('PeriodicIn', [0; 1; 0]);
model.component('comp1').physics('solid').feature('pc2').set('ComponentPeriodicType', {'AntiPeriodicity'; 'AntiPeriodicity'; 'Continuity'});
model.component('comp1').physics('solid').feature('bndl1').set('LoadType', 'TotalForce');
model.component('comp1').physics('solid').feature('bndl1').set('Ftot', {'F_x'; '0'; 'F_z'});
model.component('comp1').physics('solid').feature('bndl1').set('FperArea', {'0'; '0'; 'F_z'});

model.component('comp1').mesh('mesh1').feature('size').set('hauto', 4);
model.component('comp1').mesh('mesh1').run;

model.study.create('std1');
model.study('std1').create('stat', 'Stationary');

model.sol.create('sol1');
model.sol('sol1').study('std1');
model.sol('sol1').attach('std1');
model.sol('sol1').create('st1', 'StudyStep');
model.sol('sol1').create('v1', 'Variables');
model.sol('sol1').create('s1', 'Stationary');
model.sol('sol1').feature('s1').create('fc1', 'FullyCoupled');
model.sol('sol1').feature('s1').create('d1', 'Direct');
model.sol('sol1').feature('s1').create('i1', 'Iterative');
model.sol('sol1').feature('s1').feature('i1').create('mg1', 'Multigrid');
model.sol('sol1').feature('s1').feature('i1').feature('mg1').feature('pr').create('so1', 'SOR');
model.sol('sol1').feature('s1').feature('i1').feature('mg1').feature('po').create('so1', 'SOR');
model.sol('sol1').feature('s1').feature.remove('fcDef');

model.result.numerical.create('av5', 'AvSurface');
model.result.numerical.create('av6', 'AvSurface');
model.result.numerical('av5').selection.set([4]);
model.result.numerical('av5').set('probetag', 'none');
model.result.numerical('av6').selection.set([4]);
model.result.numerical('av6').set('probetag', 'none');
model.result.create('pg1', 'PlotGroup3D');
model.result.create('pg2', 'PlotGroup3D');
model.result('pg1').create('surf1', 'Surface');
model.result('pg1').feature('surf1').create('def', 'Deform');
model.result('pg2').create('arws1', 'ArrowSurface');
model.result('pg2').create('surf1', 'Surface');
model.result('pg2').feature('arws1').create('col', 'Color');
model.result('pg2').feature('arws1').create('def', 'Deform');
model.result('pg2').feature('arws1').feature('col').set('expr', 'comp1.solid.bndl1.F_A_Mag');
model.result('pg2').feature('surf1').set('expr', '1');
model.result('pg2').feature('surf1').create('def', 'Deform');

model.nodeGroup.create('dset1solidlgrp', 'Results');
model.nodeGroup('dset1solidlgrp').set('type', 'plotgroup');
model.nodeGroup('dset1solidlgrp').placeAfter('plotgroup', 'pg1');

model.sol('sol1').attach('std1');
model.sol('sol1').feature('s1').feature('aDef').set('cachepattern', true);
model.sol('sol1').feature('s1').feature('fc1').set('linsolver', 'd1');
model.sol('sol1').feature('s1').feature('d1').label('Suggested Direct Solver (solid)');
model.sol('sol1').feature('s1').feature('i1').label('Suggested Iterative Solver (solid)');
model.sol('sol1').feature('s1').feature('i1').set('nlinnormuse', true);
model.sol('sol1').feature('s1').feature('i1').feature('mg1').feature('pr').feature('so1').set('relax', 0.8);
model.sol('sol1').feature('s1').feature('i1').feature('mg1').feature('po').feature('so1').set('relax', 0.8);
model.sol('sol1').runAll;

model.result.numerical('av5').label('Young''s Modulus');
model.result.numerical('av5').set('table', 'tbl2');
model.result.numerical('av5').set('expr', {'(F_z*L_0)/(A*w)'});
model.result.numerical('av5').set('unit', {'N/m^2'});
model.result.numerical('av5').set('descr', {'E'});
model.result.numerical('av5').set('const', {'solid.refpntx' '0' 'Reference point for moment computation, x coordinate'; 'solid.refpnty' '0' 'Reference point for moment computation, y coordinate'; 'solid.refpntz' '0' 'Reference point for moment computation, z coordinate'});
model.result.numerical('av6').label('Poisson Ratio');
model.result.numerical('av6').set('table', 'tbl1');
model.result.numerical('av6').set('expr', {'F_x/A' 'u/L_0' '(F_x/A)/(u/L_0)' '((E)/(2*((F_x/A)/(u/L_0))))-1' 'u'});
model.result.numerical('av6').set('unit', {'N/m^2' '1' 'N/m^2' '1' 'm'});
model.result.numerical('av6').set('descr', {'Shear Stress' 'Shear Strain' 'Shear Modulus' 'Poisson Ratio' 'Displacement field, X component'});
model.result.numerical('av6').set('const', {'solid.refpntx' '0' 'Reference point for moment computation, x coordinate'; 'solid.refpnty' '0' 'Reference point for moment computation, y coordinate'; 'solid.refpntz' '0' 'Reference point for moment computation, z coordinate'});
model.result.numerical('av5').setResult;
model.result.numerical('av6').setResult;
model.result('pg1').label('Stress (solid)');
model.result('pg1').feature('surf1').set('const', {'solid.refpntx' '0' 'Reference point for moment computation, x coordinate'; 'solid.refpnty' '0' 'Reference point for moment computation, y coordinate'; 'solid.refpntz' '0' 'Reference point for moment computation, z coordinate'});
model.result('pg1').feature('surf1').set('colortable', 'RainbowLight');
model.result('pg1').feature('surf1').set('resolution', 'normal');
model.result('pg1').feature('surf1').feature('def').set('scale', 19944.10413027234);
model.result('pg1').feature('surf1').feature('def').set('scaleactive', false);
model.result('pg2').label('Boundary Loads (solid)');
model.result('pg2').set('titletype', 'custom');
model.result('pg2').set('typeintitle', false);
model.result('pg2').set('descriptionintitle', false);
model.result('pg2').set('unitintitle', false);
model.result('pg2').set('frametype', 'spatial');
model.result('pg2').set('showlegendsunit', true);
model.result('pg2').feature('arws1').label('Boundary Load 1');
model.result('pg2').feature('arws1').set('expr', {'solid.bndl1.F_Ax' 'solid.bndl1.F_Ay' 'solid.bndl1.F_Az'});
model.result('pg2').feature('arws1').set('descr', 'Load (spatial frame)');
model.result('pg2').feature('arws1').set('const', {'solid.refpntx' '0' 'Reference point for moment computation, x coordinate'; 'solid.refpnty' '0' 'Reference point for moment computation, y coordinate'; 'solid.refpntz' '0' 'Reference point for moment computation, z coordinate'});
model.result('pg2').feature('arws1').set('placement', 'gausspoints');
model.result('pg2').feature('arws1').feature('col').set('coloring', 'gradient');
model.result('pg2').feature('arws1').feature('col').set('topcolor', 'red');
model.result('pg2').feature('arws1').feature('def').set('scale', 0);
model.result('pg2').feature('arws1').feature('def').set('scaleactive', true);
model.result('pg2').feature('surf1').active(false);
model.result('pg2').feature('surf1').label('Gray Surfaces');
model.result('pg2').feature('surf1').set('const', {'solid.refpntx' '0' 'Reference point for moment computation, x coordinate'; 'solid.refpnty' '0' 'Reference point for moment computation, y coordinate'; 'solid.refpntz' '0' 'Reference point for moment computation, z coordinate'});
model.result('pg2').feature('surf1').set('coloring', 'uniform');
model.result('pg2').feature('surf1').set('color', 'gray');
model.result('pg2').feature('surf1').set('resolution', 'normal');
model.result('pg2').feature('surf1').feature('def').set('scale', 0);
model.result('pg2').feature('surf1').feature('def').set('scaleactive', true);

model.nodeGroup('dset1solidlgrp').label('Applied Loads (solid)');
model.nodeGroup('dset1solidlgrp').add('plotgroup', 'pg2');

mphsave(model,'cube_tension');

% Cube_tension.m -----------------------------------------------------------
%

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#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=4
#SBATCH --time=01:00:00
#SBATCH --mem=8G
#SBATCH --partition=regular
#SBATCH --output=cube_tension-%j.out
#SBATCH --error=cube_tension-%j.stderr

#pwd
#module purge 
module load MATLAB/2022b-r5
module load COMSOL/6.0

# Start the COMSOL server, usually on port 2036, if it is available, otherwise it will generate an error
comsol mphserver -np ${SLURM_CPUS_PER_TASK} -port 2036 -silent -tmpdir $TMPDIR &

# Run a MATLAB script called "test.m" which uses some COMSOL functions
matlab -nodisplay -r cube_tension