Example: Constrained optimizations

Download constraints.run

#!/bin/sh

# This example demonstrates the setup of all different types of constraints.
# Note that all constraints types can be combined with each other, as long as
# the resulting set of constraints actually makes sense. (It must of course be
# possible to satisfy all of them at the same time. AMS is not able to check
# that and you might get really surprising results if that is not the case ...)


# 1. Angle constraints
# ====================

AMS_JOBNAME=angle "$AMSBIN/ams" << EOF

   Task GeometryOptimization

   GeometryOptimization
      Convergence Step=1.0e-3
   End

   System
       Atoms
          O   0.001356   0.000999   0.000000
          H   0.994442  -0.037855   0.000000
          H  -0.298554   0.948531   0.000000
       End
   End

   Constraints
     # Fix the H--O--H angle to 125 degrees.
     Angle  3 1 2 125.0
   End

   Engine DFTB
       Model SCC-DFTB
       ResourcesDir Dresden
       DispersionCorrection Auto
   EndEngine

EOF


# 2. Distance constraints
# =======================

AMS_JOBNAME=dist "$AMSBIN/ams" << EOF

   Task GeometryOptimization

   GeometryOptimization
      Convergence Step=1.0e-3
   End

   System
       Atoms
          O   0.001356   0.000999   0.000000
          H   0.994442  -0.037855   0.000000
          H  -0.298554   0.948531   0.000000
       End
       BondOrders
          1 2 1.0
          1 3 1.0
       End
   End
   Constraints
      # Fix the OH bond distances to 1.03 Angstrom, for which bonds need to be defined in the System block
      All bonds O H to 1.03
      # Alternatively you can list the distances one by one as follows
      # Distance  1 2 1.03
      # Distance  1 3 1.03
   End

   Engine DFTB
       Model SCC-DFTB
       ResourcesDir Dresden
       DispersionCorrection Auto
   EndEngine

EOF


# 3. Dihedral angle constraint
# ============================

AMS_JOBNAME=dihed "$AMSBIN/ams" << EOF

   Task GeometryOptimization

   GeometryOptimization
      Convergence Step=1.0e-3
   End

   System
       Atoms
          C   -0.004115   -0.000021    0.000023
          C    1.535711    0.000022    0.000008
          H   -0.399693    1.027812   -0.000082
          H   -0.399745   -0.513934    0.890139
          H   -0.399612   -0.513952   -0.890156
          H    1.931188    0.514066    0.890140
          H    1.931432    0.513819   -0.890121
          H    1.931281   -1.027824    0.000244
       End
   End

   Constraints
      # Fix the dihedral angle H(6)--C(2)--C(1)--H(3) to 20 degrees.
      Dihedral  6 2 1 3 20.00
   End

   Engine DFTB
       Model SCC-DFTB
       ResourcesDir Dresden
       DispersionCorrection Auto
   EndEngine

EOF


# 4a. Fixed atom constraint (Atoms keyword)
# =========================================

AMS_JOBNAME=atom "$AMSBIN/ams" << EOF

   Task GeometryOptimization

   GeometryOptimization
      Convergence Energy=1.0e-6 Gradients=1.0e-4 Step=1.0e-3
      CoordinateType Cartesian
   End

   System
      Atoms
         C   -0.2460249052   -1.70363153     0.0005128649944
         O    1.152833576    -1.81594932    -0.0004409224206
         C    1.489235475     0.61782051    10.0004771689226
         O    0.5700116914    0.627761615   10.0005491194077
      End
   End

   Constraints
      # Fix atom 1 and 2 at their initial positions.
      Atom 1
      Atom 2
   End

   Engine DFTB
      Model SCC-DFTB
      ResourcesDir DFTB.org/mio-1-1
   EndEngine

EOF


# 4b. Fixed atom constraint (AtomList keyword)
# ============================================

AMS_JOBNAME=atomlist "$AMSBIN/ams" << EOF

   Task GeometryOptimization

   GeometryOptimization
      Convergence Energy=1.0e-6 Gradients=1.0e-4 Step=1.0e-3
      CoordinateType Cartesian
   End

   System
      Atoms
         C   -0.2460249052   -1.70363153     0.0005128649944
         O    1.152833576    -1.81594932    -0.0004409224206
         C    1.489235475     0.61782051    10.0004771689226
         O    0.5700116914    0.627761615   10.0005491194077
      End
   End

   Constraints
      # Fix atom 1 and 2 at their initial positions.
      AtomList 1:2
   End

   Engine DFTB
      Model SCC-DFTB
      ResourcesDir DFTB.org/mio-1-1
   EndEngine

EOF


# 4c. Fixed atom constraint (FixedRegion keyword)
# ===============================================

AMS_JOBNAME=region "$AMSBIN/ams" << EOF

   Task GeometryOptimization

   GeometryOptimization
      Convergence Energy=1.0e-6 Gradients=1.0e-4 Step=1.0e-3
      CoordinateType Cartesian
   End

   System
      Atoms
         C   -0.2460249052   -1.70363153     0.0005128649944    region=fixed
         O    1.152833576    -1.81594932    -0.0004409224206    region=fixed
         C    1.489235475     0.61782051    10.0004771689226
         O    0.5700116914    0.627761615   10.0005491194077
      End
   End

   Constraints
      # Fix all atoms in region "fixed"
      FixedRegion fixed
   End

   Engine DFTB
      Model SCC-DFTB
      ResourcesDir DFTB.org/mio-1-1
   EndEngine

EOF


# 4d. Fixed atom constraint (overlapping combination)
# ===================================================

AMS_JOBNAME=combination "$AMSBIN/ams" << EOF

   Task GeometryOptimization

   GeometryOptimization
      Convergence Energy=1.0e-6 Gradients=1.0e-4 Step=1.0e-3
      CoordinateType Cartesian
   End

   System
      Atoms
         C   -0.2460249052   -1.70363153     0.0005128649944    region=fixed
         O    1.152833576    -1.81594932    -0.0004409224206    region=fixed
         C    1.489235475     0.61782051    10.0004771689226
         O    0.5700116914    0.627761615   10.0005491194077
      End
   End

   Constraints
      Atom 1
      AtomList 1 2
      FixedRegion fixed
   End

   Engine DFTB
      Model SCC-DFTB
      ResourcesDir DFTB.org/mio-1-1
   EndEngine

EOF


# 5. Fixed coordinate constraint
# ==============================

AMS_JOBNAME=coord "$AMSBIN/ams" << EOF

   Task GeometryOptimization

   GeometryOptimization
      Convergence Energy=1.0e-6 Gradients=1.0e-4 Step=1.0e-3
      CoordinateType Cartesian
   End

   System
      Atoms
         C   -0.2460249052   -1.70363153     0.0005128649944
         O    1.152833576    -1.81594932    -0.0004409224206
         C    1.489235475     0.61782051    10.0004771689226
         O    0.5700116914    0.627761615   10.0005491194077
      End
   End

   Constraints
      # Fix the x-coordinate of all atoms.
      Coordinate 1 x
      Coordinate 2 x
      Coordinate 3 x
      Coordinate 4 x
   End

   Engine DFTB
      Model SCC-DFTB
      ResourcesDir DFTB.org/mio-1-1
   EndEngine

EOF


# 6. Fixed atom constraint (in periodic system)
# =============================================

AMS_JOBNAME=pbcatom "$AMSBIN/ams" << EOF

   Task GeometryOptimization

   GeometryOptimization
      Convergence Step=1.0e-3
   End

   System
       Atoms
           C  -1.23  -0.710140830   0.0
           C  -1.23  -0.710140830   3.8
           C   0.0    0.0           0.4
           C   0.0   -1.42028166    3.355
       End

       Lattice
           1.23  -2.130422493309719  0.0
           1.23   2.130422493309719  0.0
       End
   End

   Constraints
      # Fix atom 1 and 3 at their initial positions.
      Atom 1
      Atom 3
   End

   Engine DFTB
      Model SCC-DFTB
      ResourcesDir DFTB.org/mio-1-1
      KSpace Quality=GammaOnly
   EndEngine

EOF


# 7. Block constraints (with listing the atoms in a block)
# ========================================================

AMS_JOBNAME=block_list "$AMSBIN/ams" << EOF

   Task GeometryOptimization

   System
       Atoms
           C   0.5584839616765542   0.5023705181144142  -0.4625483159356394
           C   1.07173137896726     0.2125484528111251  -1.892767990599312
           C   1.699248504588085   -1.006061067555322   -2.191856791501442
           C   2.242484629452111   -1.236470028363516   -3.455616615521399
           C   2.18874580207099    -0.2444337131062739  -4.435483595049287
           C   1.604409798904145    0.9866950282217637  -4.135465239465763
           C   1.061086793296828    1.217355116664161   -2.871773146851866
           H   1.763625603740592   -1.780903563899969   -1.431707209662057
           H   2.716038261390732   -2.190869049673275   -3.672115451399807
           H   2.611833078693977   -0.4241619800888815  -5.420308290235123
           H   1.578029796368043    1.774138556616255   -4.884624561698751
           H   0.6247213391616491   2.187200330357715   -2.64521108544713
           C   1.303528070245188   -0.1416812092038768   0.7303699949711653
           C   0.8164830922475474  -1.314631142230651    1.326337082260565
           C   1.531799364672407   -1.947399963062604    2.342825210379356
           C   2.757684862125068   -1.432061688813837    2.765634667957531
           C   3.271640455523863   -0.2897364031184506   2.150731553729188
           C   2.556535912403799    0.3432056352653093   1.134221563049466
           H  -0.128925843064934   -1.7366201913903      0.9939642396630857
           H   1.133600273086767   -2.849990046242235    2.799740694330775
           H   3.31486005979636    -1.925049398411132    3.557912279830031
           H   4.236604921323707    0.1064455961800578   2.457138367063388
           H   2.976510069814392    1.222131876866508    0.6510413538003352
           C  -0.930165749820548    0.9153412637395284  -0.5420710991631585
           C  -1.791729737216814    0.6892660986048864   0.5418285200469819
           C  -3.111373625199894    1.139542032267652    0.5090625363459357
           C  -3.586568528476239    1.843983986018719   -0.5977864609101087
           C  -2.726152821786783    2.111108432452229   -1.663369105880468
           C  -1.406454626777386    1.660929752085611   -1.63085383469072
           H  -1.428888457076976    0.1571120160719108   1.417905619994904
           H  -3.76723983501283     0.9462006794587581   1.35432032282366
           H  -4.614972346570283    2.194578435055282   -0.6233521468909432
           H  -3.080200905921361    2.678981846821393   -2.520207901691867
           H  -0.7413545301831963   1.891248563160919   -2.459672151335554
           C   1.235557647765805    1.735720249011045    0.1803884343948648
           C   1.377191890012647    1.826646222422494    1.573181692925026
           C   1.905898822116255    2.975086608901246    2.16214311213053
           C   2.280792642899383    4.061906342938987    1.371311861877147
           C   2.105006642447361    3.998471351380415   -0.0115253875199488
           C   1.576317094651283    2.850163227898022   -0.6007264381779673
           H   1.072424817958776    0.9937816064904853   2.202306496283991
           H   2.017471491684088    3.023369029562452    3.242524256706377
           H   2.693031233132915    4.956641734238467    1.830324484771476
           H   2.372569859099136    4.8485771293401     -0.6342066225733602
           H   1.427765851939196    2.820397327218896   -1.677480576376967
       End
   End

   GeometryOptimization
       Convergence
           Energy 1.0e-6
           Gradients 1.0e-4
           Step 1.0e-4
       End
   End

   Constraints
      # Create blocks from the 4 phenyl groups by specifying the atom indices
      # explicitly. (The indices follow the order in the System%Atoms block,
      # where we happen to have the atoms belonging to the different phenyl
      # groups consecutive.)
      BlockAtoms  2  3  4  5  6  7  8  9 10 11 12
      BlockAtoms 13 14 15 16 17 18 19 20 21 22 23
      BlockAtoms 24 25 26 27 28 29 30 31 32 33 34
      BlockAtoms 35 36 37 38 39 40 41 42 43 44 45
   End

   Engine DFTB
       Model DFTB3
       ResourcesDir DFTB.org/3ob-3-1
       DispersionCorrection D3-BJ
   EndEngine

EOF


# 8. Block constraints (with named blocks)
# ========================================

AMS_JOBNAME=block_names "$AMSBIN/ams" << EOF

   Task GeometryOptimization

   System
       Atoms
           C   0.5584839616765542   0.5023705181144142  -0.4625483159356394
           C   1.07173137896726     0.2125484528111251  -1.892767990599312        region=phenyl1
           C   1.699248504588085   -1.006061067555322   -2.191856791501442        region=phenyl1
           C   2.242484629452111   -1.236470028363516   -3.455616615521399        region=phenyl1
           C   2.18874580207099    -0.2444337131062739  -4.435483595049287        region=phenyl1
           C   1.604409798904145    0.9866950282217637  -4.135465239465763        region=phenyl1
           C   1.061086793296828    1.217355116664161   -2.871773146851866        region=phenyl1
           H   1.763625603740592   -1.780903563899969   -1.431707209662057        region=phenyl1
           H   2.716038261390732   -2.190869049673275   -3.672115451399807        region=phenyl1
           H   2.611833078693977   -0.4241619800888815  -5.420308290235123        region=phenyl1
           H   1.578029796368043    1.774138556616255   -4.884624561698751        region=phenyl1
           H   0.6247213391616491   2.187200330357715   -2.64521108544713         region=phenyl1
           C   1.303528070245188   -0.1416812092038768   0.7303699949711653       region=phenyl2
           C   0.8164830922475474  -1.314631142230651    1.326337082260565        region=phenyl2
           C   1.531799364672407   -1.947399963062604    2.342825210379356        region=phenyl2
           C   2.757684862125068   -1.432061688813837    2.765634667957531        region=phenyl2
           C   3.271640455523863   -0.2897364031184506   2.150731553729188        region=phenyl2
           C   2.556535912403799    0.3432056352653093   1.134221563049466        region=phenyl2
           H  -0.128925843064934   -1.7366201913903      0.9939642396630857       region=phenyl2
           H   1.133600273086767   -2.849990046242235    2.799740694330775        region=phenyl2
           H   3.31486005979636    -1.925049398411132    3.557912279830031        region=phenyl2
           H   4.236604921323707    0.1064455961800578   2.457138367063388        region=phenyl2
           H   2.976510069814392    1.222131876866508    0.6510413538003352       region=phenyl2
           C  -0.930165749820548    0.9153412637395284  -0.5420710991631585       region=phenyl3
           C  -1.791729737216814    0.6892660986048864   0.5418285200469819       region=phenyl3
           C  -3.111373625199894    1.139542032267652    0.5090625363459357       region=phenyl3
           C  -3.586568528476239    1.843983986018719   -0.5977864609101087       region=phenyl3
           C  -2.726152821786783    2.111108432452229   -1.663369105880468        region=phenyl3
           C  -1.406454626777386    1.660929752085611   -1.63085383469072         region=phenyl3
           H  -1.428888457076976    0.1571120160719108   1.417905619994904        region=phenyl3
           H  -3.76723983501283     0.9462006794587581   1.35432032282366         region=phenyl3
           H  -4.614972346570283    2.194578435055282   -0.6233521468909432       region=phenyl3
           H  -3.080200905921361    2.678981846821393   -2.520207901691867        region=phenyl3
           H  -0.7413545301831963   1.891248563160919   -2.459672151335554        region=phenyl3
           C   1.235557647765805    1.735720249011045    0.1803884343948648       region=phenyl4
           C   1.377191890012647    1.826646222422494    1.573181692925026        region=phenyl4
           C   1.905898822116255    2.975086608901246    2.16214311213053         region=phenyl4
           C   2.280792642899383    4.061906342938987    1.371311861877147        region=phenyl4
           C   2.105006642447361    3.998471351380415   -0.0115253875199488       region=phenyl4
           C   1.576317094651283    2.850163227898022   -0.6007264381779673       region=phenyl4
           H   1.072424817958776    0.9937816064904853   2.202306496283991        region=phenyl4
           H   2.017471491684088    3.023369029562452    3.242524256706377        region=phenyl4
           H   2.693031233132915    4.956641734238467    1.830324484771476        region=phenyl4
           H   2.372569859099136    4.8485771293401     -0.6342066225733602       region=phenyl4
           H   1.427765851939196    2.820397327218896   -1.677480576376967        region=phenyl4
       End
   End

   GeometryOptimization
       Convergence
           Energy 1.0e-6
           Gradients 1.0e-4
           Step 1.0e-4
       End
   End

   Constraints
      # Use the region from System%Atoms to set up the block constraints.
      Block phenyl1
      Block phenyl2
      Block phenyl3
      Block phenyl4
   End

   Engine DFTB
       Model DFTB3
       ResourcesDir DFTB.org/3ob-3-1
       DispersionCorrection D3-BJ
   EndEngine

EOF


# 9. Frozen strain components
# ===========================

AMS_JOBNAME=freezestrain "$AMSBIN/ams" << EOF

Task GeometryOptimization

GeometryOptimization
    OptimizeLattice Yes
    Convergence Step=1.0e-3
End

Constraints
   # Keeps first two lattice vectors orthogonal to the third.  Also fixes the
   # length of the third vector, keeping the graphene layer compressed.
   FreezeStrain xz yz zz
End

System
    Atoms
        C 1.332002504889882e-05 -0.0005830055256093706 -8.209389319526933e-06
        C -1.22799350000696 -0.7102112812520209 2.281155685325205e-06
        C -0.0006872840163290542 -0.0003386565731411325 -1.981477647175959
        C 1.2274512359848 0.7092866246929653 -1.981478017299119
        C 2.455989750017203 -0.000767672446473915 -5.638209535859324e-06
        C 1.227983749989149 -0.7105220051279582 3.556077144406634e-06
        C 2.455553905980411 -0.0003697961984884611 -1.981476578954899
        C 3.68349483597652 0.7093774139714127 -1.981475303736415
        C 4.912014119974971 -0.0004697689000645081 8.202057640607653e-06
        C 3.68401303002027 -0.7103327188132248 -6.644074866545941e-06
        C 4.911561265976663 -0.0002732185613776612 -1.98147535090646
        C -3.685503114025999 0.7094747213946447 -1.98147447813657
        C -2.457004890026731 -0.0008782302621621878 8.760751751649826e-06
        C -3.684994169978904 -0.7103491590560944 -6.913500704937906e-06
        C -2.45740142402999 -0.0002120088132086839 -1.981473170030486
        C -1.229200584026242 0.709517932531879 -1.98147439816519
        C 1.227980230018157 2.127401471357515 -5.950364005944094e-06
        C 9.469984377119545e-06 1.417970232416515 5.120417805695729e-06
        C 1.227229005981529 2.127790824745807 -1.981476944534885
        C 2.45544009594217 2.837313001498961 -1.981464045820237
        C 3.683977240012926 2.127396400995821 -4.237131224100653e-06
        C 2.456019429974761 1.41770041892015 8.271514976735398e-06
        C 3.683520895940616 2.127826615636785 -1.981463536474189
        C 4.911484545967099 2.837408990674362 -1.981472216079415
        C 6.140019459971655 2.127636216669431 9.289406940173374e-06
        C 4.912011129977858 1.417969521782559 7.256699431696856e-06
        C 6.139527915931508 2.12792209328836 -1.981460550680031
        C -2.457504644023984 2.837506078460876 -1.981475136785154
        C -1.229001220032881 2.127025640069692 1.077705178964691e-05
        C -2.457025360024441 1.417788944250494 8.010947395781608e-06
        C -1.229428944072945 2.128012192586653 -1.981459091806229
        C -0.001217694074323372 2.837543459113209 -1.981458639351295
        C 2.455982410005773 4.255441598373883 -1.892083560740779e-06
        C 1.228003499971814 3.545886142064043 9.237737681677788e-06
        C 2.455221785970465 4.255792992279458 -1.981473318340598
        C -1.228386974045185 -3.547700260767117 -1.981468190394571
        C 4.911976899993052 4.255411828501257 2.27723146438149e-06
        C 3.684014579960917 3.545723396055813 1.280915829951697e-05
        C 4.911520375955087 4.255828023455356 -1.981468278811
        C 1.227655395958869 -3.547614761418386 -1.98146951906497
        C -2.457018900008975 4.255512695928259 2.943041159330732e-06
        C 6.140026009993287 3.545891232143294 2.20060806891485e-06
        C 7.367526315913146 4.255927240986645 -1.981454533470139
        C -6.141340994042006 -3.547511474074143 -1.981469232026619
        C -0.001002500050462096 4.255387679251578 1.654017565004685e-05
        C -1.228981830007242 3.545851372434187 2.37503105142233e-06
        C -0.00142595404759982 4.256013860539822 -1.981467396982039
        C -3.685044664049419 -3.547477052980626 -1.981466802486946
        C -1.227808819999351 -2.12938224692705 -2.127801149456805e-07
        C -2.455832350038186 -2.838708610558109 1.251523005803983e-05
        C -1.228620264037983 -2.129205540950233 -1.981470550283798
        C -0.0004192140835714842 -1.419477849521901 -1.981455609514733
        C 1.228193719957573 -2.129406616582517 1.390527520593389e-05
        C 0.0001477699611014405 -2.839255138681037 1.274825905530347e-05
        C 1.227684425953123 -2.129163359695275 -1.981467635427455
        C 2.455626385910209 -1.419413169537493 -1.981453570671329
        C -6.140842350045955 -2.129322170430451 1.506226938282425e-05
        C 2.456153479955113 -2.839200210115958 1.47101339575357e-05
        C 3.683689305925244 -2.129064842197087 -1.981458500475127
        C -4.913374384079035 -1.419316522220884 -1.981457095053834
        C -3.684843340052955 -2.129350560151249 1.735547419229382e-05
        C -4.912808430047692 -2.839071261955975 1.563048016823986e-05
        C -3.685268534086676 -2.128978772839927 -1.98145459141338
        C -2.45712732409351 -1.419353221465499 -1.981452351546793
        C -2.996192032925579e-05 -0.000699242152149526 3.962939886687566
        C -1.228003971875175 -0.7103778453492622 3.962925088122617
        C -0.000700355908038296 -0.0003332148789394825 1.981452859744668
        C 1.227439704045832 0.7092909964964251 1.981467977918086
        C 2.455972288079895 -0.000591484995550912 3.962939812711258
        C 1.228003298120663 -0.7104549535647978 3.962926452096982
        C 2.455542044092204 -0.0003647244468015716 1.981452779807835
        C 3.683482354040657 0.7093820057289575 1.981469673526022
        C 4.912000348117807 -0.0004686671456845799 3.96292738718769
        C 3.683997778083127 -0.7103249572456309 3.962938753391991
        C 4.911548884078128 -0.0002680168299863262 1.981457393146928
        C -3.685515265933381 0.7094801331342701 1.981461165904004
        C -2.457014661901717 -0.0008761383582568633 3.962933787286889
        C -3.685007531928472 -0.7103425373777408 3.962942555784025
        C -2.457412705931413 -0.0002065770405354501 1.981460520958165
        C -1.229211335932976 0.7095228343414065 1.98146103281522
        C 1.227967348110556 2.127386193561453 3.962929764672974
        C -4.281883530521391e-06 1.417919455416095 3.96292782690195
        C 1.227218624090811 2.127796526544795 1.981453236878594
        C 2.455427384033809 2.83731889320433 1.981471917810995
        C 3.683966438104317 2.127406352683383 3.962931809362267
        C 2.456006178071116 1.417740879775001 3.962942690498066
        C 3.683508864080636 2.127831077384122 1.981456571921596
        C 4.911472874041424 2.837414422441095 1.981469423240322
        C 6.140006188100173 2.127640908364754 3.96293316778528
        C 4.912000948062944 1.417975193600739 3.962945368689221
        C 6.139515384034993 2.127928054994523 1.981471530520008
        C -2.457516635928298 2.837511270211092 1.981459501137365
        C -1.229012451945974 2.127104470095207 3.962948291371187
        C -2.457033631907664 1.417792836176979 3.962935736248542
        C -1.229441855971066 2.128017364296635 1.981473516125039
        C -0.001231065982844282 2.83754798082405 1.981477377543141
        C 2.455970918062962 4.255446730162459 3.962945363741043
        C 1.227990978068837 3.545888883850297 3.962943437699987
        C 2.455207564067417 4.255798083939164 1.981460905296909
        C -1.228397585936881 -3.54769452897796 1.981462310609218
        C 4.911964488060532 4.255420650159205 3.962946159605713
        C 3.684002968100828 3.545727757822979 3.962932953064215
        C 4.911507194030889 4.25583213519047 1.981472875202606
        C 1.22764468406568 -3.547609799614339 1.981461473160161
        C -2.457027591902453 4.255510887977889 3.962934029953071
        C 6.140011718057854 3.545898453762834 3.962947035832434
        C 7.367513404018803 4.25593209270268 1.981476837527609
        C -6.141352815949912 -3.547506482310592 1.981466583645511
        C -0.001013701916043441 4.255385511194097 3.962938483249906
        C -1.228995721948309 3.545866003895579 3.962949056786192
        C -0.001438315946372004 4.256019262267359 1.98146542401001
        C -3.68505504595736 -3.547472521146422 1.981469025022036
        C -1.227817711946263 -2.129397354545356 3.962948386486201
        C -2.45584760189824 -2.838693919188594 3.962932647309199
        C -1.22863031596877 -2.129200899095368 1.981472763926178
        C -0.0004312259786934947 -1.419471387806733 1.981476015973903
        C 1.228183428085925 -2.129384525179524 3.962937836939656
        C 0.0001342880538246494 -2.839225227582055 3.962948356816577
        C 1.227671624025677 -2.129158527960262 1.981474583888431
        C 2.455614294015247 -1.419407657803005 1.981478001551132
        C -6.140855951953014 -2.129314868796188 3.962950599781267
        C 2.456139408049645 -2.839212628030558 3.962949726809414
        C 3.683677514018658 -2.12905939044384 1.98147688315868
        C -4.913386125957436 -1.419311390469788 1.981469050050141
        C -3.68485488196171 -2.129348928295441 3.96295344930467
        C -4.91282016191732 -2.839063750265042 3.962938899273355
        C -3.685281025994509 -2.12897353111013 1.981481200585353
        C -2.457141595966529 -1.419347949824808 1.981472029890663
    End
    Lattice
        9.825000579999999 0.0 0.0
        4.91182904 8.51302256 0.0
        0.0 0.0 8.0
    End
End

Engine DFTB
    Model DFTB
    ResourcesDir DFTB.org/mio-1-1
    KSpace
        Quality GammaOnly
    End
EndEngine

EOF


# 10. Equalized strain components
# ===============================

AMS_JOBNAME=equalstrain "$AMSBIN/ams" << EOF

Task GeometryOptimization

GeometryOptimization
    OptimizeLattice Yes
    Convergence Step=1.0e-3
End

Constraints
   # Keep the cell cubic, but allow the size of the cube to vary.
   FreezeStrain xy xz yz
   EqualStrain  xx yy zz
End

System
    Atoms
        C -0.132285 3.230196 3.399625
        H 0.67231 2.571995 3.747816
        H -0.546925 3.782407 4.25108
        H -0.921872 2.627955 2.935193
        H 0.267346 3.938428 2.664409
        C 2.647972 3.79511 0.161215
        H 2.745753 2.707187 0.254494
        H 2.108302 4.189352 1.030219
        H 2.093026 4.03506 -0.753279
        H 3.644808 4.248843 0.113424
        C -3.290954 -3.607704 -3.419879
        H -4.099867 -4.000479 -4.046956
        H -2.386445 -3.482146 -4.026458
        H -3.088346 -4.309774 -2.602634
        H -3.589157 -2.638419 -3.003466
        C -3.900392 1.971446 -2.092972
        H -2.821972 1.97396 -1.895882
        H -4.303924 2.977719 -1.930439
        H -4.394183 1.265761 -1.414725
        H -4.081488 1.668344 -3.130841
        C -3.143958 -3.520015 3.393796
        H -3.128547 -4.088022 2.456262
        H -3.994325 -3.845525 4.004334
        H -3.24151 -2.450891 3.171766
        H -2.211449 -3.695621 3.94282
        C -0.31406 -0.626145 3.522914
        H -0.044022 0.228271 4.154493
        H -1.353702 -0.912447 3.720437
        H 0.346904 -1.471041 3.749005
        H -0.205421 -0.349364 2.467723
        C 3.411151 -3.454122 0.161835
        H 2.877462 -2.569463 0.528433
        H 4.211866 -3.141886 -0.518755
        H 2.711585 -4.107617 -0.372385
        H 3.843691 -3.997522 1.010048
        H -3.283653 -0.451758 -4.172013
        H -1.922139 0.6502520000000001 -3.802207
        H -2.586463 -0.412172 -2.523601
        C -2.360175 -0.332772 -3.593334
        H -1.648446 -1.117408 -3.875514
        C 3.046249 -3.33059 3.76859
        H 2.414628 -3.18136 2.88506
        H 2.465863 -3.831302 4.55235
        H 3.39517 -2.358701 4.136729
        H 3.909333 -3.950995 3.500222
        C -3.086408 3.73574 0.4638
        H -2.559805 3.990117 -0.463465
        H -2.394025 3.813016 1.310247
        H -3.469203 2.710618 0.397221
        H -3.922599 4.429208 0.611196
        C 3.736451 0.338903 -0.234383
        H 4.139844 -0.659226 -0.441391
        H 4.286082 0.789262 0.6004350000000001
        H 2.675343 0.256879 0.028602
        H 3.844535 0.968696 -1.125179
        C -0.953217 3.761489 -3.029722
        H -0.738671 2.687271 -2.986546
        H -2.017033 3.913231 -3.24677
        H -0.349572 4.223228 -3.819817
        H -0.707592 4.222226 -2.065757
        C 3.438238 3.368005 3.536049
        H 3.718968 3.030104 2.531632
        H 4.305113 3.831685 4.021198
        H 3.102844 2.509703 4.129906
        H 2.62603 4.10053 3.461459
        C -0.093351 2.447961 0.147782
        H 0.412783 2.191741 -0.790311
        H -1.100739 2.015519 0.149423
        H -0.163522 3.53817 0.239205
        H 0.478074 2.046413 0.99281
        C -0.06737899999999999 -1.067744 -0.644773
        H 0.831493 -1.69444 -0.611303
        H -0.920384 -1.630791 -0.248288
        H -0.271712 -0.77696 -1.681851
        H 0.091087 -0.168785 -0.037648
        C -3.13266 0.095347 1.684164
        H -2.468956 -0.758832 1.506078
        H -3.797646 -0.127993 2.526632
        H -3.731911 0.285949 0.786162
        H -2.532126 0.982263 1.917783
        C -3.650862 -2.700373 -0.074687
        H -4.155919 -2.467829 0.87013
        H -2.740814 -3.276506 0.129574
        H -3.385824 -1.767849 -0.58654
        H -4.32089 -3.289309 -0.711913
        C 3.803884 3.754796 -3.348637
        H 3.946713 2.667857 -3.350306
        H 2.769436 3.987861 -3.626912
        H 4.48894 4.214494 -4.07059
        H 4.010448 4.148971 -2.34674
        C 2.868209 0.11231 2.894284
        H 2.317604 0.914041 2.388417
        H 2.406222 -0.09055000000000001 3.867554
        H 3.909847 0.420825 3.041412
        H 2.839161 -0.7950739999999999 2.279753
        C -0.320765 -3.560008 1.887422
        H -0.965068 -2.68183 2.011986
        H 0.02585 -3.901247 2.869895
        H 0.543227 -3.294315 1.26713
        H -0.88707 -4.36264 1.400678
        C 2.415398 -1.437717 -2.776235
        H 1.964383 -1.676188 -3.746573
        H 2.445411 -2.340763 -2.155392
        H 1.816728 -0.668767 -2.274091
        H 3.43507 -1.065149 -2.928883
        C -3.625996 2.934989 3.78523
        H -4.070333 2.734452 2.803299
        H -3.043299 2.064066 4.107404
        H -4.421782 3.131813 4.513121
        H -2.968572 3.809626 3.717096
        C 1.422335 1.538945 -3.931672
        H 0.608488 0.8054 -3.894205
        H 2.3282 1.060135 -4.321529
        H 1.616409 1.921293 -2.92272
        H 1.136242 2.368954 -4.588236
        C 0.028875 -3.521123 -2.677443
        H 0.240436 -2.624091 -3.271089
        H -0.857142 -3.347281 -2.055678
        H 0.888225 -3.744967 -2.034598
        H -0.156019 -4.368152 -3.348409
    End
    Lattice
        10.0 0.0 0.0
        0.0 10.0 0.0
        0.0 0.0 10.0
    End
End

Engine DFTB
    Model DFTB
    ResourcesDir DFTB.org/mio-1-1
    KSpace
        Quality GammaOnly
    End
EndEngine

EOF