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Added activeAtomMask to energy calculations
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25 changes: 0 additions & 25 deletions
25
include/cando/chem/energy_functions/_AnchorRestraint_debugEvalDeclares.cc
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,28 +1,3 @@ | ||
| /* | ||
| File: _AnchorRestraint_debugEvalDeclares.cc | ||
| */ | ||
| /* | ||
| Open Source License | ||
| Copyright (c) 2016, Christian E. Schafmeister | ||
| Permission is hereby granted, free of charge, to any person obtaining a copy | ||
| of this software and associated documentation files (the "Software"), to deal | ||
| in the Software without restriction, including without limitation the rights | ||
| to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | ||
| copies of the Software, and to permit persons to whom the Software is | ||
| furnished to do so, subject to the following conditions: | ||
| The above copyright notice and this permission notice shall be included in | ||
| all copies or substantial portions of the Software. | ||
| THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | ||
| IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | ||
| FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | ||
| AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | ||
| LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | ||
| OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | ||
| THE SOFTWARE. | ||
| This is an open source license for the CANDO software from Temple University, but it is not the only one. Contact Temple University at mailto:[email protected] if you would like a different license. | ||
| */ | ||
| /* -^- */ | ||
| // DEFINE_EVAL | ||
| struct { | ||
| double x1; | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,28 +1,3 @@ | ||
| /* | ||
| File: _AnchorRestraint_debugEvalSerialize.cc | ||
| */ | ||
| /* | ||
| Open Source License | ||
| Copyright (c) 2016, Christian E. Schafmeister | ||
| Permission is hereby granted, free of charge, to any person obtaining a copy | ||
| of this software and associated documentation files (the "Software"), to deal | ||
| in the Software without restriction, including without limitation the rights | ||
| to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | ||
| copies of the Software, and to permit persons to whom the Software is | ||
| furnished to do so, subject to the following conditions: | ||
| The above copyright notice and this permission notice shall be included in | ||
| all copies or substantial portions of the Software. | ||
| THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | ||
| IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | ||
| FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | ||
| AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | ||
| LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | ||
| OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | ||
| THE SOFTWARE. | ||
| This is an open source license for the CANDO software from Temple University, but it is not the only one. Contact Temple University at mailto:[email protected] if you would like a different license. | ||
| */ | ||
| /* -^- */ | ||
| // XML_EVAL | ||
| node->attributeIfNotDefault("evalx1", this->eval.x1, 0.0 ); | ||
| node->attributeIfNotDefault("evaly1", this->eval.y1, 0.0 ); | ||
|
|
@@ -42,3 +17,4 @@ This is an open source license for the CANDO software from Temple University, bu | |
| node->attributeIfNotDefault("evalohx1z1", this->eval.ohx1z1, 0.0 ); | ||
| node->attributeIfNotDefault("evalohy1z1", this->eval.ohy1z1, 0.0 ); | ||
| node->attributeIfNotDefault("evalAnchorDeviation", this->eval.AnchorDeviation, 0.0 ); | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,28 +1,3 @@ | ||
| /* | ||
| File: _AnchorRestraint_debugEvalSet.cc | ||
| */ | ||
| /* | ||
| Open Source License | ||
| Copyright (c) 2016, Christian E. Schafmeister | ||
| Permission is hereby granted, free of charge, to any person obtaining a copy | ||
| of this software and associated documentation files (the "Software"), to deal | ||
| in the Software without restriction, including without limitation the rights | ||
| to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | ||
| copies of the Software, and to permit persons to whom the Software is | ||
| furnished to do so, subject to the following conditions: | ||
| The above copyright notice and this permission notice shall be included in | ||
| all copies or substantial portions of the Software. | ||
| THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | ||
| IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | ||
| FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | ||
| AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | ||
| LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | ||
| OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | ||
| THE SOFTWARE. | ||
| This is an open source license for the CANDO software from Temple University, but it is not the only one. Contact Temple University at mailto:[email protected] if you would like a different license. | ||
| */ | ||
| /* -^- */ | ||
| // SET_EVAL | ||
| EVAL_SET(x1, x1); | ||
| EVAL_SET(y1, y1); | ||
|
|
@@ -42,3 +17,4 @@ This is an open source license for the CANDO software from Temple University, bu | |
| EVAL_SET(ohx1z1, ohx1z1); | ||
| EVAL_SET(ohy1z1, ohy1z1); | ||
| EVAL_SET(AnchorDeviation, AnchorDeviation); | ||
|
|
||
79 changes: 27 additions & 52 deletions
79
include/cando/chem/energy_functions/_AnchorRestraint_debugFiniteDifference.cc
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,83 +1,58 @@ | ||
| /* | ||
| File: _AnchorRestraint_debugFiniteDifference.cc | ||
| */ | ||
| /* | ||
| Open Source License | ||
| Copyright (c) 2016, Christian E. Schafmeister | ||
| Permission is hereby granted, free of charge, to any person obtaining a copy | ||
| of this software and associated documentation files (the "Software"), to deal | ||
| in the Software without restriction, including without limitation the rights | ||
| to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | ||
| copies of the Software, and to permit persons to whom the Software is | ||
| furnished to do so, subject to the following conditions: | ||
| The above copyright notice and this permission notice shall be included in | ||
| all copies or substantial portions of the Software. | ||
| THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | ||
| IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | ||
| FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | ||
| AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | ||
| LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | ||
| OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | ||
| THE SOFTWARE. | ||
| This is an open source license for the CANDO software from Temple University, but it is not the only one. Contact Temple University at mailto:[email protected] if you would like a different license. | ||
| */ | ||
| /* -^- */ | ||
| // FINITE_DIFFERENCE_TEST | ||
| TEST_FORCE( _evaluateEnergyOnly_AnchorRestraint, delta2*2.0, | ||
| (-delta2 + x1, y1, z1, xa, ya, za, ka), | ||
| (delta2 + x1, y1, z1, xa, ya, za, ka), | ||
| (ENERGY_FUNCTION, -delta2 + x1, y1, z1, xa, ya, za, ka), | ||
| (ENERGY_FUNCTION, delta2 + x1, y1, z1, xa, ya, za, ka), | ||
| fx1, | ||
| index); | ||
| TEST_FORCE( _evaluateEnergyOnly_AnchorRestraint, delta2*2.0, | ||
| (x1, -delta2 + y1, z1, xa, ya, za, ka), | ||
| (x1, delta2 + y1, z1, xa, ya, za, ka), | ||
| (ENERGY_FUNCTION, x1, -delta2 + y1, z1, xa, ya, za, ka), | ||
| (ENERGY_FUNCTION, x1, delta2 + y1, z1, xa, ya, za, ka), | ||
| fy1, | ||
| index); | ||
| TEST_FORCE( _evaluateEnergyOnly_AnchorRestraint, delta2*2.0, | ||
| (x1, y1, -delta2 + z1, xa, ya, za, ka), | ||
| (x1, y1, delta2 + z1, xa, ya, za, ka), | ||
| (ENERGY_FUNCTION, x1, y1, -delta2 + z1, xa, ya, za, ka), | ||
| (ENERGY_FUNCTION, x1, y1, delta2 + z1, xa, ya, za, ka), | ||
| fz1, | ||
| index); | ||
| TEST_DIAGONAL_HESSIAN( _evaluateEnergyOnly_AnchorRestraint, delta2*2.0, | ||
| (-delta2 + x1, y1, z1, xa, ya, za, ka), | ||
| (x1, y1, z1, xa, ya, za, ka), | ||
| (delta2 + x1, y1, z1, xa, ya, za, ka), | ||
| (ENERGY_FUNCTION, -delta2 + x1, y1, z1, xa, ya, za, ka), | ||
| (ENERGY_FUNCTION, x1, y1, z1, xa, ya, za, ka), | ||
| (ENERGY_FUNCTION, delta2 + x1, y1, z1, xa, ya, za, ka), | ||
| dhx1x1, | ||
| index); | ||
| TEST_OFF_DIAGONAL_HESSIAN( _evaluateEnergyOnly_AnchorRestraint, | ||
| delta2*2.0, | ||
| (-delta2 + x1, -delta2 + y1, z1, xa, ya, za, ka), | ||
| (delta2 + x1, -delta2 + y1, z1, xa, ya, za, ka), | ||
| (-delta2 + x1, delta2 + y1, z1, xa, ya, za, ka), | ||
| (delta2 + x1, delta2 + y1, z1, xa, ya, za, ka), | ||
| (ENERGY_FUNCTION, -delta2 + x1, -delta2 + y1, z1, xa, ya, za, ka), | ||
| (ENERGY_FUNCTION, delta2 + x1, -delta2 + y1, z1, xa, ya, za, ka), | ||
| (ENERGY_FUNCTION, -delta2 + x1, delta2 + y1, z1, xa, ya, za, ka), | ||
| (ENERGY_FUNCTION, delta2 + x1, delta2 + y1, z1, xa, ya, za, ka), | ||
| ohx1y1, | ||
| index); | ||
| TEST_OFF_DIAGONAL_HESSIAN( _evaluateEnergyOnly_AnchorRestraint, | ||
| delta2*2.0, | ||
| (-delta2 + x1, y1, -delta2 + z1, xa, ya, za, ka), | ||
| (delta2 + x1, y1, -delta2 + z1, xa, ya, za, ka), | ||
| (-delta2 + x1, y1, delta2 + z1, xa, ya, za, ka), | ||
| (delta2 + x1, y1, delta2 + z1, xa, ya, za, ka), | ||
| (ENERGY_FUNCTION, -delta2 + x1, y1, -delta2 + z1, xa, ya, za, ka), | ||
| (ENERGY_FUNCTION, delta2 + x1, y1, -delta2 + z1, xa, ya, za, ka), | ||
| (ENERGY_FUNCTION, -delta2 + x1, y1, delta2 + z1, xa, ya, za, ka), | ||
| (ENERGY_FUNCTION, delta2 + x1, y1, delta2 + z1, xa, ya, za, ka), | ||
| ohx1z1, | ||
| index); | ||
| TEST_DIAGONAL_HESSIAN( _evaluateEnergyOnly_AnchorRestraint, delta2*2.0, | ||
| (x1, -delta2 + y1, z1, xa, ya, za, ka), | ||
| (x1, y1, z1, xa, ya, za, ka), | ||
| (x1, delta2 + y1, z1, xa, ya, za, ka), | ||
| (ENERGY_FUNCTION, x1, -delta2 + y1, z1, xa, ya, za, ka), | ||
| (ENERGY_FUNCTION, x1, y1, z1, xa, ya, za, ka), | ||
| (ENERGY_FUNCTION, x1, delta2 + y1, z1, xa, ya, za, ka), | ||
| dhy1y1, | ||
| index); | ||
| TEST_OFF_DIAGONAL_HESSIAN( _evaluateEnergyOnly_AnchorRestraint, | ||
| delta2*2.0, | ||
| (x1, -delta2 + y1, -delta2 + z1, xa, ya, za, ka), | ||
| (x1, delta2 + y1, -delta2 + z1, xa, ya, za, ka), | ||
| (x1, -delta2 + y1, delta2 + z1, xa, ya, za, ka), | ||
| (x1, delta2 + y1, delta2 + z1, xa, ya, za, ka), | ||
| (ENERGY_FUNCTION, x1, -delta2 + y1, -delta2 + z1, xa, ya, za, ka), | ||
| (ENERGY_FUNCTION, x1, delta2 + y1, -delta2 + z1, xa, ya, za, ka), | ||
| (ENERGY_FUNCTION, x1, -delta2 + y1, delta2 + z1, xa, ya, za, ka), | ||
| (ENERGY_FUNCTION, x1, delta2 + y1, delta2 + z1, xa, ya, za, ka), | ||
| ohy1z1, | ||
| index); | ||
| TEST_DIAGONAL_HESSIAN( _evaluateEnergyOnly_AnchorRestraint, delta2*2.0, | ||
| (x1, y1, -delta2 + z1, xa, ya, za, ka), | ||
| (x1, y1, z1, xa, ya, za, ka), | ||
| (x1, y1, delta2 + z1, xa, ya, za, ka), | ||
| (ENERGY_FUNCTION, x1, y1, -delta2 + z1, xa, ya, za, ka), | ||
| (ENERGY_FUNCTION, x1, y1, z1, xa, ya, za, ka), | ||
| (ENERGY_FUNCTION, x1, y1, delta2 + z1, xa, ya, za, ka), | ||
| dhz1z1, | ||
| index); |
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