#!/usr/bin/env amspython
from scm.bert import check_output
from scm.plams import AMSJob, AMSResults
# 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 ...)
def check_results(results: AMSResults):
assert results.ok(), results.get_errormsg()
assert check_output(results, NLines=(2, "Total Energy (hartree)"))
assert check_output(
results,
From="Total Gradients (hartree/bohr)",
To="Total Gradients (eV/angstrom)",
filter_options=("$ERROR 1.0e-3",),
)
assert check_output(
results,
From="Mulliken Charges",
ToRE=r"^\s*$",
filter_options=("$ERROR 1.0e-3",),
)
# 1. Angle constraints
# ====================
def test_angle_constraints():
results = AMSJob.from_input(
"""
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
""",
name="angle",
).run()
check_results(results)
# 2. Distance constraints
# =======================
def test_distance_constraints():
results = AMSJob.from_input(
"""
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
""",
name="dist",
).run()
check_results(results)
# 3. Dihedral angle constraint
# ============================
def test_dihedral_angle_constraint():
results = AMSJob.from_input(
"""
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
""",
name="dihed",
).run()
check_results(results)
# 4a. Fixed atom constraint (Atoms keyword)
# =========================================
def test_fixed_atom_constraint_atoms_keyword():
results = AMSJob.from_input(
"""
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
""",
name="atom",
).run()
check_results(results)
# 4b. Fixed atom constraint (AtomList keyword)
# ============================================
def test_fixed_atom_constraint_atomlist_keyword():
results = AMSJob.from_input(
"""
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
""",
name="atomlist",
).run()
check_results(results)
# 4c. Fixed atom constraint (FixedRegion keyword)
# ===============================================
def test_fixed_atom_constraint_fixed_region_keyword():
results = AMSJob.from_input(
"""
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
""",
name="region",
).run()
check_results(results)
# 4d. Fixed atom constraint (overlapping combination)
# ===================================================
def test_fixed_atom_constraint_overlapping_combination():
results = AMSJob.from_input(
"""
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
""",
name="combination",
).run()
check_results(results)
# 5. Fixed coordinate constraint
# ==============================
def test_fixed_coordinate_constraint():
results = AMSJob.from_input(
"""
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
""",
name="coord",
).run()
check_results(results)
# 6. Fixed atom constraint (in periodic system)
# =============================================
def test_fixed_atom_constraint_in_periodic_system():
results = AMSJob.from_input(
"""
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
""",
name="pbcatom",
).run()
check_results(results)
# 7. Block constraints (with listing the atoms in a block)
# ========================================================
def test_block_constraints_with_explicit_atom_lists():
results = AMSJob.from_input(
"""
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
CoordinateType Delocalized
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
""",
name="block_list",
).run()
check_results(results)
# 8. Block constraints (with named blocks)
# ========================================
def test_block_constraints_with_named_blocks():
results = AMSJob.from_input(
"""
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
CoordinateType Delocalized
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
""",
name="block_names",
).run()
check_results(results)
# 9. Frozen strain components
# ===========================
def test_frozen_strain_components():
results = AMSJob.from_input(
"""
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
""",
name="freezestrain",
).run()
check_results(results)
# 10. Equalized strain components
# ===============================
def test_equalized_strain_components():
results = AMSJob.from_input(
"""
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
""",
name="equalstrain",
).run()
check_results(results)
