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Commit f0160f8a authored by dmar's avatar dmar
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Adding the folder for the 4th exercise

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Exercises/Exercise-4/Analysis/Cluster-Analysis.ipynb 0 → 100644
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Exercises/Exercise-4/Analysis/Crystal-Analysis.ipynb 0 → 100644
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Exercises/Exercise-4/Exercise-4-cluster/150atoms.xyz 0 → 100644
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150
optimized
Ar 0.145255 -5.37377e-07 -0.190435
Ar 0.153937 9.5964e-06 3.3332
Ar 1.1194 -3.00016 1.38854
Ar -2.40298 -1.85665 1.3829
Ar -2.40298 1.85666 1.38289
Ar 1.1194 3.00017 1.38853
Ar 3.29927 4.2234e-06 1.38749
Ar -0.832984 -3.00056 -1.7644
Ar -3.01232 -5.28286e-06 -1.76296
Ar -0.832984 3.00055 -1.76442
Ar 2.69371 1.85454 -1.76606
Ar 2.69371 -1.85455 -1.76605
Ar 0.139693 -1.06711e-05 -3.71414
Ar 0.141042 1.99928e-05 6.94868
Ar 1.14785 -3.07014 5.03427
Ar -2.44391 -1.90547 5.01805
Ar -2.44391 1.9055 5.01804
Ar 1.14785 3.07017 5.03425
Ar 3.37355 1.47215e-05 5.0362
Ar 4.369 -3.06888 3.03937
Ar 2.11766 -6.07445 3.00647
Ar -1.46793 -4.96955 3.03907
Ar -5.01877 -3.74669 3.01301
Ar -5.06808 8.31626e-06 3.01645
Ar -5.01877 3.74671 3.01299
Ar -1.46793 4.96957 3.03904
Ar 2.11766 6.07446 3.00644
Ar 4.369 3.0689 3.03935
Ar 6.53025 9.105e-06 3.00554
Ar 3.75034 -4.96685 -0.18846
Ar 0.140694 -6.13919 -0.185784
Ar -3.4683 -4.96808 -0.182442
Ar -5.69604 -1.8994 -0.185953
Ar -5.69604 1.8994 -0.185964
Ar -3.4683 4.96807 -0.182471
Ar 0.140693 6.13919 -0.185819
Ar 3.75034 4.96685 -0.188488
Ar 5.98059 1.89732 -0.189687
Ar 5.98059 -1.89733 -0.189676
Ar 1.75292 -4.96717 -3.41434
Ar -1.83626 -6.07519 -3.37605
Ar -4.08566 -3.07031 -3.40947
Ar -6.24786 -1.01457e-05 -3.37439
Ar -4.08567 3.07029 -3.40949
Ar -1.83626 6.07517 -3.37608
Ar 1.75292 4.96715 -3.41437
Ar 5.30677 3.75465 -3.383
Ar 5.36187 -9.4473e-06 -3.41697
Ar 5.30677 -3.75467 -3.38298
Ar -0.860003 -3.06985 -5.40737
Ar -3.08982 -1.57645e-05 -5.40585
Ar -0.860003 3.06982 -5.40739
Ar 2.7488 1.89741 -5.41011
Ar 2.7488 -1.89744 -5.4101
Ar 0.135986 -2.10613e-05 -7.32703
Ar 0.0909943 3.07294e-05 10.6834
Ar 1.15073 -3.10923 8.74023
Ar -2.50219 -1.93499 8.71556
Ar -2.50219 1.93504 8.71555
Ar 1.15072 3.10929 8.74021
Ar 3.40227 2.53886e-05 8.7448
Ar 4.45201 -3.1282 6.78492
Ar 2.16265 -6.20116 6.73346
Ar -1.49225 -5.06812 6.78119
Ar -5.10105 -3.8221 6.73327
Ar -5.11504 1.89233e-05 6.706
Ar -5.10105 3.82214 6.73325
Ar -1.49225 5.06816 6.78116
Ar 2.16265 6.2012 6.73342
Ar 4.45201 3.12824 6.7849
Ar 6.66249 1.98386e-05 6.73471
Ar 7.67509 -3.11181 4.70872
Ar 5.43165 -6.20037 4.70847
Ar 3.15044 -9.2512 4.67668
Ar -0.488532 -8.12627 4.71126
Ar -4.12143 -6.93752 4.71888
Ar -7.72272 -5.67376 4.72344
Ar -7.76588 -1.8871 4.70065
Ar -7.76588 1.88712 4.70064
Ar -7.72272 5.67379 4.72341
Ar -4.12143 6.93754 4.71884
Ar -0.488533 8.1263 4.71121
Ar 3.15044 9.25122 4.67662
Ar 5.43165 6.2004 4.70843
Ar 7.67509 3.11184 4.70871
Ar 9.86998 1.41432e-05 4.67537
Ar 7.11173 -5.06348 1.45592
Ar 4.80477 -8.12503 1.4357
Ar 1.14466 -9.31329 1.43855
Ar -2.52336 -8.19324 1.46443
Ar -6.14929 -6.93568 1.45932
Ar -8.40339 -3.82827 1.45278
Ar -8.4719 3.59214e-06 1.45741
Ar -8.40339 3.82827 1.45276
Ar -6.1493 6.93568 1.45928
Ar -2.52336 8.19325 1.46438
Ar 1.14466 9.3133 1.4385
Ar 4.80477 8.12504 1.43565
Ar 7.11173 5.06349 1.45589
Ar 9.30993 1.92346 1.43409
Ar 9.30993 -1.92345 1.4341
Ar 6.42669 -6.94551 -1.81359
Ar 2.8013 -8.19343 -1.83188
Ar -0.866243 -9.31395 -1.8062
Ar -4.52678 -8.12488 -1.79994
Ar -6.83143 -5.06504 -1.82158
Ar -9.02857 -1.92511 -1.80272
Ar -9.02857 1.9251 -1.80273
Ar -6.83143 5.06502 -1.82161
Ar -4.52678 8.12486 -1.79999
Ar -0.866244 9.31394 -1.80626
Ar 2.80129 8.19342 -1.83192
Ar 6.42668 6.9455 -1.81363
Ar 8.68823 3.83296 -1.81488
Ar 8.75526 -4.66125e-06 -1.83614
Ar 8.68823 -3.83297 -1.81486
Ar 4.4013 -6.94584 -5.08473
Ar 0.768581 -8.1256 -5.08085
Ar -2.87137 -9.2519 -5.04313
Ar -5.15174 -6.20213 -5.07499
Ar -7.39428 -3.11293 -5.07459
Ar -9.58998 -1.51754e-05 -5.04118
Ar -7.39428 3.1129 -5.0746
Ar -5.15174 6.2021 -5.07503
Ar -2.87137 9.25187 -5.04319
Ar 0.76858 8.12558 -5.08089
Ar 4.4013 6.94582 -5.08477
Ar 8.00771 5.71823 -5.05474
Ar 8.06093 1.90928 -5.08753
Ar 8.06093 -1.90931 -5.08752
Ar 8.00771 -5.71826 -5.05471
Ar 1.78085 -5.06436 -7.1559
Ar -1.88033 -6.20216 -7.10132
Ar -4.17194 -3.12996 -7.15077
Ar -6.38473 -2.08671e-05 -7.09918
Ar -4.17194 3.12992 -7.15079
Ar -1.88033 6.20211 -7.10136
Ar 1.78084 5.06432 -7.15593
Ar 5.41142 3.83317 -7.10847
Ar 5.46041 -2.0201e-05 -7.15879
Ar 5.41142 -3.83321 -7.10845
Ar -0.877312 -3.1129 -9.11103
Ar -3.13841 -2.64186e-05 -9.10944
Ar -0.877313 3.11284 -9.11105
Ar 2.782 1.92387 -9.11407
Ar 2.782 -1.92392 -9.11405
Ar 0.132753 -3.18006e-05 -11.0614
Ar -5.20814 2.9699e-05 10.4554
Ar -7.83183 1.90516 8.45414
Ar -7.83183 -1.90511 8.45416
Exercises/Exercise-4/Exercise-4-cluster/38atoms.xyz 0 → 100644
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38
i = 28, E = -0.0621020546
Ar 4.5837264705 -2.5298506230 2.8419660895
Ar -5.0883572196 1.9357723701 2.4184523727
Ar -3.2418290672 -0.9829937359 -3.1034656658
Ar 1.5707910149 -3.2049904251 -2.8927286085
Ar 0.5840025577 1.8005740161 5.6483922753
Ar -2.4373564514 -5.1009421235 1.8780648647
Ar -4.5837253441 2.5298503599 -2.8419663316
Ar 2.9180022935 -0.5181600301 -5.1676140994
Ar -1.5707898886 3.2049901620 2.8927283664
Ar 4.5971833659 3.6902063075 0.8577619876
Ar -0.5840014314 -1.8005742793 -5.6483925174
Ar -1.9062811555 1.7092250875 -5.3788535870
Ar -3.7461702873 4.6289241801 0.1633966928
Ar 1.9327257081 4.5068538706 3.3823535937
Ar 5.0883583459 -1.9357726333 -2.4184526148
Ar 5.9259034057 0.1633001792 0.5869154140
Ar 2.4373575777 5.1009418603 -1.8780651068
Ar 1.5957315683 2.9916413419 -4.8980751725
Ar -0.2271030843 5.9175894252 0.6465175007
Ar -1.0673712050 3.7976425265 -2.3549703161
Ar 3.7452488788 1.5756428373 -2.1442332599
Ar -2.9180011672 0.5181597669 5.1676138573
Ar -1.9327245817 -4.5068541338 -3.3823538358
Ar -5.9259022794 -0.1633004424 -0.5869156561
Ar 1.9062822818 -1.7092253506 5.3788533449
Ar 3.7461714136 -4.6289244433 -0.1633969349
Ar -3.7452477525 -1.5756431005 2.1442330178
Ar -4.5971822395 -3.6902065706 -0.8577622297
Ar 0.2271042106 -5.9175896884 -0.6465177428
Ar 1.0673723313 -3.7976427897 2.3549700740
Ar -1.5957304419 -2.9916416051 4.8980749304
Ar 1.0829442695 2.3808945811 0.3727739264
Ar 3.2418301935 0.9829934728 3.1034654237
Ar 0.2507144477 0.2951564708 -2.6135044442
Ar 2.3968228644 -1.1066203188 0.1049515634
Ar -2.3968217381 1.1066200557 -0.1049518055
Ar -0.2507133214 -0.2951567339 2.6135042021
Ar -1.0829431432 -2.3808948442 -0.3727741686
Exercises/Exercise-4/Exercise-4-cluster/450atoms.xyz 0 → 100644
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Exercises/Exercise-4/Exercise-4-cluster/817atoms.xyz 0 → 100644
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Exercises/Exercise-4/Exercise-4-cluster/templ_production.inp 0 → 100644
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@SET SIZE _MYSIZE_
&GLOBAL
PRINT_LEVEL SILENT
PROJECT production_${SIZE}
RUN_TYPE MD
&END GLOBAL
&EXT_RESTART
RESTART_FILE_NAME thermalization_${SIZE}-1.restart
&END
&MOTION
&MD
ENSEMBLE NVE
STEPS 10000
&PRINT
&ENERGY SILENT
&EACH
MD 10
&END
&END
&END
&END MD
&PRINT
&RESTART
&EACH
MD 0
&END
&END
&RESTART_HISTORY OFF
&END
&TRAJECTORY on
FORMAT xyz
&EACH
MD 100
&END EACH
&END TRAJECTORY
&END PRINT
&END MOTION
&FORCE_EVAL
METHOD Fist
STRESS_TENSOR ANALYTICAL
&MM
&FORCEFIELD
&CHARGE
ATOM Ar
CHARGE 0.0
&END
&NONBONDED
&LENNARD-JONES
atoms Ar Ar
EPSILON 119.8
SIGMA 3.405
RCUT 8.4
&END LENNARD-JONES
&END NONBONDED
&END FORCEFIELD
&POISSON
PERIODIC NONE
&EWALD
EWALD_TYPE none
&END EWALD
&END POISSON
&PRINT
&FF_INFO OFF
SPLINE_DATA
SPLINE_INFO
&END FF_INFO
&END PRINT
&END MM
&PRINT
&FORCES off
&END FORCES
&GRID_INFORMATION
&END GRID_INFORMATION
&END PRINT
&SUBSYS
&CELL
ABC 150 150 150
PERIODIC NONE
&END CELL
&TOPOLOGY
COORD_FILE_NAME ${SIZE}atoms.xyz
COORDINATE xyz
&CENTER_COORDINATES
&END
&END
&END SUBSYS
&END FORCE_EVAL
Exercises/Exercise-4/Exercise-4-cluster/templ_thermalization.inp 0 → 100644
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@SET SIZE _MYSIZE_
&GLOBAL
PRINT_LEVEL SILENT
PROJECT thermalization_${SIZE}
RUN_TYPE MD
&END GLOBAL
&MOTION
&MD
ENSEMBLE NVT
STEPS 100000
TIMESTEP 0.5 !fs
TEMPERATURE 20.0 ! K
&PRINT
&ENERGY SILENT
&EACH
MD 10
&END
&END
&END
&THERMOSTAT
TYPE CSVR
&CSVR
TIMECON 5000
&END
&END THERMOSTAT
&END MD
&PRINT
&RESTART
&EACH
MD 0
&END
&END
&RESTART_HISTORY OFF
&END
&TRAJECTORY on
FORMAT xyz
&EACH
MD 1000
&END EACH
&END TRAJECTORY
&END PRINT
&END MOTION
&FORCE_EVAL
METHOD Fist
STRESS_TENSOR ANALYTICAL
&MM
&FORCEFIELD
&CHARGE
ATOM Ar
CHARGE 0.0
&END
&NONBONDED
&LENNARD-JONES
atoms Ar Ar
EPSILON 119.8
SIGMA 3.405
RCUT 8.4
&END LENNARD-JONES
&END NONBONDED
&END FORCEFIELD
&POISSON
PERIODIC NONE
&EWALD
EWALD_TYPE none
&END EWALD
&END POISSON
&PRINT
&FF_INFO OFF
SPLINE_DATA
SPLINE_INFO
&END FF_INFO
&END PRINT
&END MM
&PRINT
&FORCES off
&END FORCES
&GRID_INFORMATION
&END GRID_INFORMATION
&END PRINT
&SUBSYS
&CELL
ABC 150 150 150
PERIODIC NONE
&END CELL
&TOPOLOGY
COORD_FILE_NAME ${SIZE}atoms.xyz
COORDINATE xyz
&CENTER_COORDINATES
&END
&END
&END SUBSYS
&END FORCE_EVAL
Exercises/Exercise-4/Exercise-4-crystal/crystal_6x6.xyz 0 → 100644
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Exercises/Exercise-4/Exercise-4-crystal/jobs_production_bulk 0 → 100644
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for i in 400; do sed "s/_MYTEMP_/$i/g" < templ_production_bulk.inp > production_bulk_${i}.inp ; bsub -W 10 -R light cp2k.popt -o production_bulk_${i}.out -i production_bulk_${i}.inp; done
Exercises/Exercise-4/Exercise-4-crystal/jobs_thermalization_bulk 0 → 100644
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for i in 400; do sed "s/_MYTEMP_/$i/g" < templ_thermalization_bulk.inp > thermalization_bulk_${i}.inp ; bsub -W 10 -R light cp2k.popt -o thermalization_bulk_${i}.out -i thermalization_bulk_${i}.inp; done
Exercises/Exercise-4/Exercise-4-crystal/templ_production_bulk.inp 0 → 100644
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@SET TEMP _MYTEMP_
&GLOBAL
PRINT_LEVEL SILENT
PROJECT production_bulk_${TEMP}
RUN_TYPE MD
&END GLOBAL
&EXT_RESTART
RESTART_FILE_NAME thermalization_bulk_${TEMP}-1.restart
&END
&MOTION
&MD
&PRINT
&ENERGY SILENT
&EACH
MD 10
&END
&END
&END
ENSEMBLE NVE
STEPS 10000
TIMESTEP 0.5 !fs
&END MD
&PRINT
&RESTART
&EACH
MD 0
&END
&END
&RESTART_HISTORY OFF
&END
&TRAJECTORY on
FORMAT xyz
&EACH
MD 100
&END EACH
&END TRAJECTORY
&END PRINT
&END MOTION
&FORCE_EVAL
METHOD Fist
STRESS_TENSOR ANALYTICAL
&MM
&FORCEFIELD
&CHARGE
ATOM Ar
CHARGE 0.0
&END
&NONBONDED
&LENNARD-JONES
atoms Ar Ar
EPSILON 119.8
SIGMA 3.405
RCUT 8.4
&END LENNARD-JONES
&END NONBONDED
&END FORCEFIELD
&POISSON
PERIODIC NONE
&EWALD
EWALD_TYPE none
&END EWALD
&END POISSON
&PRINT
&FF_INFO OFF
SPLINE_DATA
SPLINE_INFO
&END FF_INFO
&END PRINT
&END MM
&PRINT
&FORCES off
&END FORCES
&GRID_INFORMATION
&END GRID_INFORMATION
&END PRINT
&SUBSYS
&CELL
ABC 31.614 31.614 31.614
&END CELL
&TOPOLOGY
COORD_FILE_NAME crystal_6x6.xyz
COORDINATE xyz
&CENTER_COORDINATES
&END
&END
&END SUBSYS
&END FORCE_EVAL
Exercises/Exercise-4/Exercise-4-crystal/templ_thermalization_bulk.inp 0 → 100644
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@SET TEMP _MYTEMP_
&GLOBAL
PRINT_LEVEL SILENT
PROJECT thermalization_bulk_${TEMP}
RUN_TYPE MD
&END GLOBAL
&MOTION
&MD
&PRINT
&ENERGY SILENT
&EACH
MD 10
&END
&END
&END
ENSEMBLE NVT
STEPS 100000
TIMESTEP 0.5 !fs
TEMPERATURE ${TEMP} !K
&THERMOSTAT
TYPE CSVR
&CSVR
TIMECON 2000
&END
&END THERMOSTAT
&END MD
&PRINT
&RESTART
&EACH
MD 0
&END
&END
&RESTART_HISTORY OFF
&END
&TRAJECTORY on
FORMAT xyz
&EACH
MD 1000
&END EACH
&END TRAJECTORY
&END PRINT
&END MOTION
&FORCE_EVAL
METHOD Fist
STRESS_TENSOR ANALYTICAL
&MM
&FORCEFIELD
&CHARGE
ATOM Ar
CHARGE 0.0
&END
&NONBONDED
&LENNARD-JONES
atoms Ar Ar
EPSILON 119.8
SIGMA 3.405
RCUT 8.4
&END LENNARD-JONES
&END NONBONDED
&END FORCEFIELD
&POISSON
PERIODIC NONE
&EWALD
EWALD_TYPE none
&END EWALD
&END POISSON
&PRINT
&FF_INFO OFF
SPLINE_DATA
SPLINE_INFO
&END FF_INFO
&END PRINT
&END MM
&PRINT
&FORCES off
&END FORCES
&GRID_INFORMATION
&END GRID_INFORMATION
&END PRINT
&SUBSYS
&CELL
ABC 31.614 31.614 31.614
&END CELL
&TOPOLOGY
COORD_FILE_NAME crystal_6x6.xyz
COORDINATE xyz
&CENTER_COORDINATES
&END
&END
&END SUBSYS
&END FORCE_EVAL
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