├── README.md ├── ala2 ├── .DS_Store ├── 1_unbiased │ ├── INPUTS.A │ └── INPUTS.B ├── 2_training_model │ ├── model.pt │ └── training.png └── 3_enhanced_sampling │ ├── ala2.tpr │ └── plumed.dat ├── aldol ├── .DS_Store ├── 1_unbiased │ ├── INPUTS.P │ ├── INPUTS.R │ ├── inp.Aldol_pm6-P │ └── inp.Aldol_pm6-R ├── 2_training_model │ ├── full_model.pt │ └── model.pt └── 3_enhanced_sampling │ ├── Aldol_pm6.inp │ ├── Contacts.cpp │ └── plumed.dat └── code ├── PytorchModel.cpp └── Tutorial - DeepLDA training.ipynb /README.md: -------------------------------------------------------------------------------- 1 | # Data-driven collective variables for enhanced sampling 2 | #### Luigi Bonati, Valerio Rizzi, and Michele Parrinello, _J. Phys. Chem. Lett._ 11, 2998-3004 (2020). 3 | 4 | [![DOI](http://img.shields.io/badge/DOI-10.1021%2Facs.jpclett.0c00535-yellow)](https://doi.org/10.1021/acs.jpclett.0c00535) 5 | [![arXiv](https://img.shields.io/badge/arXiv-2002.06562-critical)](https://arxiv.org/abs/2002.06562) 6 | [![plumID:20.004](https://img.shields.io/badge/plumID-20.004-blue)](https://www.plumed-nest.org/eggs/20/004/) 7 | [![MaterialsCloud](https://img.shields.io/badge/MaterialsCloud-2020.0035-lightgrey)](https://doi.org/10.24435/materialscloud:2020.0035/v1) 8 | 9 | > [!IMPORTANT] 10 | > This repository is kept as supporting material for the manuscript, but it is no longer updated. Check out the [mlcolvar](https://mlcolvar.readthedocs.io) library for data-driven CVs, where you can find up-to-date tutorials and examples. 11 | > 12 | > [

](https://mlcolvar.readthedocs.io) 13 | 14 | 15 | This repository contains: 16 | 1. the code necessary to train and use a neural-network collective variable optimized with Fisher's discriminant analysis 17 | 2. input file to reproduce the simulations reported in the paper 18 | 19 | #### Requirements 20 | - Pytorch and LibTorch (v == 1.4) 21 | - PLUMED2 22 | 23 | #### Tutorial 24 | Here you can find a [Google Colab notebook](https://colab.research.google.com/drive/1dG0ohT75R-UZAFMf_cbYPNQwBaOsVaAA) with the code and instructions for Deep-LDA CV training and export. 25 | 26 | #### Code and results availability 27 | The code and input files are available also on the [PLUMED-NEST](https://www.plumed-nest.org/eggs/20/004/) archive while the results of the simulations are available in the [Materials Cloud repository](https://archive.materialscloud.org/2020.0035/v1). 28 | 29 | #### Errata 30 | There is a typo in the definition of $\widetilde{\mathbf{w}}_i$ below eq. 7. The correct formula is 31 | $\widetilde{\mathbf{w}}_i=\mathbf{L}^T \mathbf{w}_i$ . 32 | 33 | #### Contact 34 | If you have comments or questions please send an email to luigi bonati [at] phys chem ethz ch . 35 | -------------------------------------------------------------------------------- /ala2/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luigibonati/data-driven-CVs/0f2f50c66bd5e3f8bacc5fd07e7350e93ff6742d/ala2/.DS_Store -------------------------------------------------------------------------------- /ala2/2_training_model/model.pt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luigibonati/data-driven-CVs/0f2f50c66bd5e3f8bacc5fd07e7350e93ff6742d/ala2/2_training_model/model.pt -------------------------------------------------------------------------------- /ala2/2_training_model/training.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luigibonati/data-driven-CVs/0f2f50c66bd5e3f8bacc5fd07e7350e93ff6742d/ala2/2_training_model/training.png -------------------------------------------------------------------------------- /ala2/3_enhanced_sampling/ala2.tpr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luigibonati/data-driven-CVs/0f2f50c66bd5e3f8bacc5fd07e7350e93ff6742d/ala2/3_enhanced_sampling/ala2.tpr -------------------------------------------------------------------------------- /ala2/3_enhanced_sampling/plumed.dat: -------------------------------------------------------------------------------- 1 | # vim:ft=plumed 2 | 3 | #DEFINE INPUTS: DISTANCES 4 | d1: DISTANCE ATOMS=2,5 5 | d2: DISTANCE ATOMS=2,6 6 | d3: DISTANCE ATOMS=2,7 7 | d4: DISTANCE ATOMS=2,9 8 | d5: DISTANCE ATOMS=2,11 9 | d6: DISTANCE ATOMS=2,15 10 | d7: DISTANCE ATOMS=2,16 11 | d8: DISTANCE ATOMS=2,17 12 | d9: DISTANCE ATOMS=2,19 13 | d10: DISTANCE ATOMS=5,6 14 | d11: DISTANCE ATOMS=5,7 15 | d12: DISTANCE ATOMS=5,9 16 | d13: DISTANCE ATOMS=5,11 17 | d14: DISTANCE ATOMS=5,15 18 | d15: DISTANCE ATOMS=5,16 19 | d16: DISTANCE ATOMS=5,17 20 | d17: DISTANCE ATOMS=5,19 21 | d18: DISTANCE ATOMS=6,7 22 | d19: DISTANCE ATOMS=6,9 23 | d20: DISTANCE ATOMS=6,11 24 | d21: DISTANCE ATOMS=6,15 25 | d22: DISTANCE ATOMS=6,16 26 | d23: DISTANCE ATOMS=6,17 27 | d24: DISTANCE ATOMS=6,19 28 | d25: DISTANCE ATOMS=7,9 29 | d26: DISTANCE ATOMS=7,11 30 | d27: DISTANCE ATOMS=7,15 31 | d28: DISTANCE ATOMS=7,16 32 | d29: DISTANCE ATOMS=7,17 33 | d30: DISTANCE ATOMS=7,19 34 | d31: DISTANCE ATOMS=9,11 35 | d32: DISTANCE ATOMS=9,15 36 | d33: DISTANCE ATOMS=9,16 37 | d34: DISTANCE ATOMS=9,17 38 | d35: DISTANCE ATOMS=9,19 39 | d36: DISTANCE ATOMS=11,15 40 | d37: DISTANCE ATOMS=11,16 41 | d38: DISTANCE ATOMS=11,17 42 | d39: DISTANCE ATOMS=11,19 43 | d40: DISTANCE ATOMS=15,16 44 | d41: DISTANCE ATOMS=15,17 45 | d42: DISTANCE ATOMS=15,19 46 | d43: DISTANCE ATOMS=16,17 47 | d44: DISTANCE ATOMS=16,19 48 | d45: DISTANCE ATOMS=17,19 49 | 50 | #LOAD PYTORCH MODEL 51 | deep: PYTORCH_MODEL FILE=../2_training_model/model.pt ARG=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15,d16,d17,d18,d19,d20,d21,d22,d23,d24,d25,d26,d27,d28,d29,d30,d31,d32,d33,d34,d35,d36,d37,d38,d39,d40,d41,d42,d43,d44,d45 52 | 53 | #DEFINE OPES CALCULATION 54 | OPES_METAD ... 55 | LABEL=opes 56 | ARG=deep.node-0 57 | PACE=500 58 | SIGMA=0.025 59 | BARRIER=30 60 | ... OPES_METAD 61 | 62 | #MONITOR DIHEDRAL ANGLES 63 | phi: TORSION ATOMS=5,7,9,15 64 | psi: TORSION ATOMS=7,9,15,17 65 | 66 | #PRINT 67 | PRINT STRIDE=500 ARG=deep.node-0,phi,psi,opes.* FILE=COLVAR 68 | 69 | ENDPLUMED 70 | 71 | #alternative: WT-METAD CALCULATION 72 | METAD ... 73 | LABEL=meta 74 | ARG=deep.node-0 75 | PACE=500 76 | HEIGHT=1.25 77 | SIGMA=0.025 78 | BIASFACTOR=6.00 79 | TEMP=300.0 80 | GRID_MIN=-2 81 | GRID_MAX=2 82 | GRID_BIN=750 83 | CALC_RCT 84 | ... METAD 85 | -------------------------------------------------------------------------------- /aldol/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luigibonati/data-driven-CVs/0f2f50c66bd5e3f8bacc5fd07e7350e93ff6742d/aldol/.DS_Store -------------------------------------------------------------------------------- /aldol/1_unbiased/inp.Aldol_pm6-P: -------------------------------------------------------------------------------- 1 | &GLOBAL 2 | PROJECT Aldol_pm6_P 3 | RUN_TYPE MD 4 | &END GLOBAL 5 | 6 | #&EXT_RESTART 7 | #RESTART_FILE_NAME Aldol_pm6_P-1.restart 8 | #&END 9 | 10 | &MOTION 11 | &MD 12 | ENSEMBLE NVT 13 | STEPS 10000000 14 | TIMESTEP 0.5 15 | TEMPERATURE 300 16 | &THERMOSTAT 17 | &CSVR 18 | TIMECON 100 19 | &END 20 | &END THERMOSTAT 21 | &END MD 22 | &PRINT 23 | &VELOCITIES OFF 24 | &END 25 | &FORCES 26 | &EACH 27 | MD 200 28 | &END 29 | &END 30 | &TRAJECTORY 31 | &EACH 32 | MD 200 33 | &END 34 | &END 35 | &RESTART 36 | &EACH 37 | MD 200 38 | &END 39 | &END 40 | &RESTART_HISTORY 41 | &EACH 42 | MD 20000 43 | &END 44 | &END 45 | &END PRINT 46 | 47 | &FREE_ENERGY 48 | &METADYN 49 | USE_PLUMED .TRUE. 50 | PLUMED_INPUT_FILE ./plumed.dat 51 | &END METADYN 52 | &END FREE_ENERGY 53 | 54 | &END MOTION 55 | 56 | &FORCE_EVAL 57 | METHOD Quickstep 58 | &DFT 59 | &QS 60 | METHOD PM6 61 | &SE 62 | &END 63 | &END QS 64 | &SCF 65 | SCF_GUESS ATOMIC 66 | # SCF_GUESS RESTART 67 | &END SCF 68 | &END DFT 69 | &SUBSYS 70 | &CELL 71 | ABC 15.0 15.0 15.0 72 | PERIODIC NONE 73 | &END CELL 74 | &COORD 75 | C -1.7398459870 1.1338848810 2.2335126395 76 | H -2.5828441792 1.7963437143 2.0707686162 77 | H -2.1967426647 0.1002722800 2.2184518098 78 | C -0.9120671394 1.4445501695 1.0289301080 79 | H -1.3917437438 1.0910381640 0.1579462762 80 | O 0.1430652785 1.9656639332 0.9898175075 81 | H -2.0915615390 3.1244075320 3.6611573450 82 | C -1.0171291761 1.4112560790 3.5721405872 83 | H -0.0051832519 1.7402738743 3.4158576545 84 | H -1.0077374295 0.6475586503 4.3768979920 85 | O -1.7899346604 2.4130111648 4.2532004479 86 | &END COORD 87 | &END SUBSYS 88 | &END FORCE_EVAL 89 | 90 | -------------------------------------------------------------------------------- /aldol/1_unbiased/inp.Aldol_pm6-R: -------------------------------------------------------------------------------- 1 | &GLOBAL 2 | PROJECT Aldol_pm6_R 3 | RUN_TYPE MD 4 | &END GLOBAL 5 | 6 | #&EXT_RESTART 7 | #RESTART_FILE_NAME Aldol_pm6_R-1.restart 8 | #&END 9 | 10 | &MOTION 11 | &MD 12 | ENSEMBLE NVT 13 | STEPS 10000000 14 | TIMESTEP 0.5 15 | TEMPERATURE 300 16 | &THERMOSTAT 17 | &CSVR 18 | TIMECON 100 19 | &END 20 | &END THERMOSTAT 21 | &END MD 22 | &PRINT 23 | &VELOCITIES OFF 24 | &END 25 | &FORCES 26 | &EACH 27 | MD 200 28 | &END 29 | &END 30 | &TRAJECTORY 31 | &EACH 32 | MD 200 33 | &END 34 | &END 35 | &RESTART 36 | &EACH 37 | MD 200 38 | &END 39 | &END 40 | &RESTART_HISTORY 41 | &EACH 42 | MD 20000 43 | &END 44 | &END 45 | &END PRINT 46 | 47 | &FREE_ENERGY 48 | &METADYN 49 | USE_PLUMED .TRUE. 50 | PLUMED_INPUT_FILE ./plumed.dat 51 | &END METADYN 52 | &END FREE_ENERGY 53 | 54 | &END MOTION 55 | 56 | &FORCE_EVAL 57 | METHOD Quickstep 58 | &DFT 59 | &QS 60 | METHOD PM6 61 | &SE 62 | &END 63 | &END QS 64 | &SCF 65 | SCF_GUESS ATOMIC 66 | # SCF_GUESS RESTART 67 | &END SCF 68 | &END DFT 69 | &SUBSYS 70 | &CELL 71 | ABC 15.0 15.0 15.0 72 | PERIODIC NONE 73 | &END CELL 74 | &COORD 75 | C -1.82559014 1.24990204 1.15842648 76 | H -1.29242639 0.32219712 1.15842648 77 | H -2.89559014 1.24990204 1.15842648 78 | C -1.15031583 2.42487933 1.15842648 79 | H -1.68347958 3.35258425 1.15842648 80 | O 0.27968417 2.42487933 1.15842648 81 | H 0.60013876 3.32981517 1.15840911 82 | C -1.75435327 0.62506239 4.36185501 83 | H -1.22118953 -0.30264253 4.36185501 84 | H -2.82435327 0.62506239 4.36185501 85 | O -1.12731284 1.71611273 4.36185501 86 | &END COORD 87 | &END SUBSYS 88 | &END FORCE_EVAL 89 | 90 | -------------------------------------------------------------------------------- /aldol/2_training_model/full_model.pt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luigibonati/data-driven-CVs/0f2f50c66bd5e3f8bacc5fd07e7350e93ff6742d/aldol/2_training_model/full_model.pt -------------------------------------------------------------------------------- /aldol/2_training_model/model.pt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luigibonati/data-driven-CVs/0f2f50c66bd5e3f8bacc5fd07e7350e93ff6742d/aldol/2_training_model/model.pt -------------------------------------------------------------------------------- /aldol/3_enhanced_sampling/Aldol_pm6.inp: -------------------------------------------------------------------------------- 1 | &GLOBAL 2 | PROJECT Aldol_pm6_R 3 | RUN_TYPE MD 4 | PRINT_LEVEL SILENT 5 | &END GLOBAL 6 | 7 | !&EXT_RESTART 8 | !RESTART_FILE_NAME Aldol_pm6_R-1.restart 9 | !&END 10 | 11 | &MOTION 12 | &MD 13 | ENSEMBLE NVT 14 | STEPS 20000000 15 | TIMESTEP 0.5 16 | TEMPERATURE 300 17 | &THERMOSTAT 18 | &CSVR 19 | TIMECON 100 20 | &END 21 | &END THERMOSTAT 22 | &END MD 23 | &PRINT 24 | &VELOCITIES OFF 25 | &END 26 | &FORCES 27 | &EACH 28 | MD 4000 29 | &END 30 | &END 31 | &TRAJECTORY 32 | &EACH 33 | MD 20 34 | &END 35 | &END 36 | &RESTART 37 | &EACH 38 | MD 1000 39 | &END 40 | &END 41 | &RESTART_HISTORY 42 | &EACH 43 | MD 50000 44 | &END 45 | &END 46 | &END PRINT 47 | 48 | &FREE_ENERGY 49 | &METADYN 50 | USE_PLUMED .TRUE. 51 | PLUMED_INPUT_FILE ./plumed.dat 52 | &END METADYN 53 | &END FREE_ENERGY 54 | 55 | &END MOTION 56 | 57 | &FORCE_EVAL 58 | METHOD Quickstep 59 | &DFT 60 | &QS 61 | METHOD PM6 62 | &END QS 63 | &SCF 64 | SCF_GUESS ATOMIC 65 | # SCF_GUESS RESTART 66 | &END SCF 67 | &END DFT 68 | &SUBSYS 69 | &CELL 70 | ABC 15.0 15.0 15.0 71 | PERIODIC NONE 72 | &END CELL 73 | &COORD 74 | C -0.4380529066 1.0289817184 2.4218640806 75 | H -0.8258218827 -0.0042005318 2.5547137238 76 | H 0.6310002384 0.9815436318 2.6588469857 77 | C -0.7536249062 1.4649971834 0.9661402699 78 | H -0.4400493227 0.6859268302 0.2052006415 79 | O -1.3955297332 2.4535993157 0.7293392173 80 | H -2.5800939393 1.4446323568 4.1921888754 81 | C -0.9189573958 2.0559768551 3.4418190661 82 | H -1.5189990031 2.8768450679 3.0258842458 83 | H -0.1063157930 2.5344538387 3.9092283136 84 | O -1.7006634559 1.5032705498 4.4766189541 85 | &END COORD 86 | &END SUBSYS 87 | &END FORCE_EVAL 88 | 89 | -------------------------------------------------------------------------------- /aldol/3_enhanced_sampling/Contacts.cpp: -------------------------------------------------------------------------------- 1 | /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2 | Copyright (c) 2011-2018 The plumed team 3 | (see the PEOPLE file at the root of the distribution for a list of names) 4 | 5 | See http://www.plumed.org for more information. 6 | 7 | This file is part of plumed, version 2. 8 | 9 | plumed is free software: you can redistribute it and/or modify 10 | it under the terms of the GNU Lesser General Public License as published by 11 | the Free Software Foundation, either version 3 of the License, or 12 | (at your option) any later version. 13 | 14 | plumed is distributed in the hope that it will be useful, 15 | but WITHOUT ANY WARRANTY; without even the implied warranty of 16 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 17 | GNU Lesser General Public License for more details. 18 | 19 | You should have received a copy of the GNU Lesser General Public License 20 | along with plumed. If not, see . 21 | +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ 22 | #include "core/Colvar.h" 23 | #include "core/ActionRegister.h" 24 | #include "tools/Pbc.h" 25 | 26 | #include 27 | #include 28 | 29 | #include 30 | #include 31 | #include 32 | 33 | #include "tools/Tools.h" 34 | #include "tools/SwitchingFunction.h" 35 | #include 36 | 37 | using namespace std; 38 | 39 | namespace PLMD { 40 | namespace colvar { 41 | 42 | 43 | class Contacts : public Colvar { 44 | bool components; 45 | bool reorderon; 46 | bool pbc; 47 | SwitchingFunction switchingFunction; 48 | bool twogroups; 49 | 50 | public: 51 | static void registerKeywords( Keywords& keys ); 52 | explicit Contacts(const ActionOptions&); 53 | //active methods: 54 | virtual void calculate(); 55 | vector atomsa; 56 | vector atomsb; 57 | int num_atomsa; 58 | int num_atomsb; 59 | int num_dist; 60 | }; 61 | 62 | PLUMED_REGISTER_ACTION(Contacts,"CONTACTS") 63 | 64 | void Contacts::registerKeywords( Keywords& keys ) { 65 | Colvar::registerKeywords( keys ); 66 | keys.addFlag("REORDER",false,"reorder the list of contacts"); 67 | keys.addFlag("COMPONENTS",true,"calculate the x, y and z components of the Contacts separately and store them as label.x, label.y and label.z"); 68 | keys.add("atoms","GROUPA","First list of atoms"); 69 | keys.add("atoms","GROUPB","Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)"); 70 | keys.add("compulsory","NN","6","The n parameter of the switching function "); 71 | keys.add("compulsory","MM","0","The m parameter of the switching function; 0 implies 2*NN"); 72 | keys.add("compulsory","D_0","0.0","The d_0 parameter of the switching function"); 73 | keys.add("compulsory","R_0","The r_0 parameter of the switching function"); 74 | keys.add("optional","SWITCH","This keyword is used if you want to employ an alternative to the continuous swiching function defined above. " 75 | "The following provides information on the \\ref switchingfunction that are available. " 76 | "When this keyword is present you no longer need the NN, MM, D_0 and R_0 keywords."); 77 | keys.addOutputComponent("c", "default", "contacts"); 78 | } 79 | 80 | Contacts::Contacts(const ActionOptions&ao): 81 | PLUMED_COLVAR_INIT(ao), 82 | components(true), 83 | reorderon(false), 84 | pbc(true), 85 | twogroups(true) 86 | { 87 | parseAtomList("GROUPA",atomsa); 88 | parseAtomList("GROUPB",atomsb); 89 | num_atomsa = atomsa.size(); 90 | num_atomsb = atomsb.size(); 91 | 92 | vector atoms; 93 | for(unsigned int i=0; i0){ 116 | num_dist = num_atomsa*num_atomsb; 117 | } else { 118 | num_dist = (num_atomsa*(num_atomsa-1))/2; 119 | twogroups = false; 120 | } 121 | 122 | log.printf(" between two groups of %u and %u atoms\n",static_cast(num_atomsa),static_cast(num_atomsb)); 123 | log.printf(" first group:\n"); 124 | for(unsigned int i=0;i0){ 142 | switchingFunction.set(sw,errors); 143 | if( errors.length()!=0 ) error("problem reading SWITCH keyword : " + errors ); 144 | } else { 145 | double r_0=-1.0, d_0; int nn, mm; 146 | parse("NN",nn); parse("MM",mm); 147 | parse("R_0",r_0); parse("D_0",d_0); 148 | if( r_0<0.0 ) error("you must set a value for R_0"); 149 | switchingFunction.set(nn,mm,r_0,d_0); 150 | } 151 | 152 | //log.printf(" Tetrahedral order parameter calculated computing the angles with the atoms within %s\n",( switchingFunction.description() ).c_str() ); 153 | 154 | if(components) { 155 | for(int i=0; i atom_pos=getPositions(); 174 | int N_atoms = atom_pos.size(); 175 | 176 | std::vector dist(num_dist); 177 | std::vector invdist(num_dist); 178 | std::vector distmod(num_dist); 179 | double sw, df, df2; //switching functions and derivatives 180 | 181 | int ind = 0; 182 | if(twogroups) { 183 | for(int i=0; i indices(num_dist); 211 | std::iota(begin(indices), end(indices), 0); 212 | std::sort(begin(indices), end(indices), 213 | [&distmod](int lhs, int rhs) { return distmod[lhs] < distmod[rhs]; }); 214 | //std::copy(begin(indices), end(indices), std::ostream_iterator(std::cout, " ")); 215 | std::vector indicesnew(num_dist); 216 | for(int k=0; k A = {6.5, 2.2, 5.6, 7.1}; 223 | std::array indices; 224 | std::iota(begin(indices), end(indices), 0); // initialize the index array 225 | // sort with custom comparator, that compares items not by their own value 226 | // but by the value of the corresponding entries in the original array. 227 | std::sort(begin(indices), end(indices), 228 | [&A](int lhs, int rhs) { return A[lhs] < A[rhs]; }); 229 | std::copy(begin(indices), end(indices), std::ostream_iterator(std::cout, " ")); 230 | */ 231 | 232 | if(components) { 233 | int ind = 0; 234 | if(twogroups) { 235 | for(int i=0; iset(sw); 258 | } 259 | else{ 260 | auto label = "c-"+std::to_string(ind); //NON REORDERED 261 | 262 | Value* val=getPntrToComponent(label); 263 | setAtomsDerivatives (val,i,-invdist[ind]*dist[ind]*df2); 264 | setAtomsDerivatives (val,j+num_atomsa,invdist[ind]*dist[ind]*df2); 265 | setBoxDerivativesNoPbc(val); 266 | val->set(sw); 267 | } 268 | 269 | ind = ind+1; 270 | } 271 | } 272 | } else{ 273 | for(int i=0; iset(sw); 296 | } 297 | else{ 298 | auto label = "c-"+std::to_string(ind); //NON REORDERED 299 | 300 | Value* val=getPntrToComponent(label); 301 | setAtomsDerivatives (val,i,-invdist[ind]*dist[ind]*df2); 302 | setAtomsDerivatives (val,j,invdist[ind]*dist[ind]*df2); 303 | setBoxDerivativesNoPbc(val); 304 | val->set(sw); 305 | } 306 | 307 | ind = ind+1; 308 | } 309 | 310 | } 311 | } 312 | } 313 | 314 | } 315 | 316 | } 317 | } 318 | 319 | 320 | 321 | -------------------------------------------------------------------------------- /aldol/3_enhanced_sampling/plumed.dat: -------------------------------------------------------------------------------- 1 | # vim:ft=plumed 2 | 3 | #UNITS 4 | UNITS LENGTH=A 5 | 6 | #LOAD FILES 7 | LOAD FILE=Contacts.cpp 8 | 9 | #DEFINE GROUP OF ATOMS 10 | C: GROUP ATOMS=1,4,8 11 | O: GROUP ATOMS=6,11 12 | H: GROUP ATOMS=2,3,5,7,9,10 13 | 14 | #DEFINE CONTACTS 15 | cc2: CONTACTS GROUPA=C SWITCH={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8} 16 | oo2: CONTACTS GROUPA=O SWITCH={RATIONAL D_0=0.0 R_0=1.6 NN=6 MM=8} 17 | co2: CONTACTS GROUPA=C GROUPB=O SWITCH={RATIONAL D_0=0.0 R_0=1.6 NN=6 MM=8} 18 | ch2: CONTACTS GROUPA=C GROUPB=H SWITCH={RATIONAL D_0=0.0 R_0=1.2 NN=6 MM=8} 19 | oh2: CONTACTS GROUPA=O GROUPB=H SWITCH={RATIONAL D_0=0.0 R_0=1.2 NN=6 MM=8} 20 | 21 | #LOAD PYTHORCH MODEL 22 | auto: PYTORCH_MODEL FILE=../2_training_model/model.pt ARG=cc2.*,oo2.*,co2.*,ch2.*,oh2.* 23 | NNcube: MATHEVAL ARG=auto.node-0 FUNC=x+x^3 PERIODIC=NO 24 | 25 | #DEFINE WALLS WALLS 26 | com1: COM ATOMS=1-7 27 | com2: COM ATOMS=8-11 28 | dc1: DISTANCE ATOMS=com1,com2 NOPBC 29 | UPPER_WALLS ARG=dc1 AT=+5.0 KAPPA=150.0 EXP=2 LABEL=uwall_1 30 | 31 | nnuw: UPPER_WALLS ARG=NNcube AT=3.2 KAPPA=2000.0 EXP=2 32 | nnlw: LOWER_WALLS ARG=NNcube AT=-3.2 KAPPA=2000.0 EXP=2 33 | 34 | #OPES CALCULATION 35 | OPES_METAD ... 36 | LABEL=opes 37 | ARG=NNcube 38 | PACE=500 39 | BARRIER=160 40 | SIGMA=0.10 41 | TEMP=300 42 | ... OPES_METAD 43 | 44 | #MONITOR DISTANCES 45 | c1c8: DISTANCE ATOMS=1,8 NOPBC 46 | o6h7: DISTANCE ATOMS=6,7 NOPBC 47 | o11h7: DISTANCE ATOMS=11,7 NOPBC 48 | 49 | #PRINT 50 | PRINT STRIDE=20 FILE=COLVAR ARG=* 51 | FLUSH STRIDE=1000 52 | -------------------------------------------------------------------------------- /code/PytorchModel.cpp: -------------------------------------------------------------------------------- 1 | /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2 | Copyright (c) 2011-2018 The plumed team 3 | (see the PEOPLE file at the root of the distribution for a list of names) 4 | 5 | See http://www.plumed.org for more information. 6 | 7 | This file is part of plumed, version 2. 8 | 9 | plumed is free software: you can redistribute it and/or modify 10 | it under the terms of the GNU Lesser General Public License as published by 11 | the Free Software Foundation, either version 3 of the License, or 12 | (at your option) any later version. 13 | 14 | plumed is distributed in the hope that it will be useful, 15 | but WITHOUT ANY WARRANTY; without even the implied warranty of 16 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 17 | GNU Lesser General Public License for more details. 18 | 19 | You should have received a copy of the GNU Lesser General Public License 20 | along with plumed. If not, see . 21 | +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ 22 | #include "function/Function.h" 23 | #include "core/ActionRegister.h" 24 | 25 | #include 26 | #include 27 | 28 | #include 29 | 30 | using namespace std; 31 | 32 | std::vector tensor_to_vector(const torch::Tensor& x) { 33 | return std::vector(x.data(), x.data() + x.numel()); 34 | } 35 | 36 | namespace PLMD { 37 | namespace function { 38 | 39 | //+PLUMEDOC FUNCTION PYTORCH MODEL 40 | /* 41 | Load a model trained with Pytorch. The derivatives are set using native backpropagation in Pytorch. 42 | 43 | \par Examples 44 | Define a model that takes as inputs two distances d1 and d2 45 | 46 | \plumedfile 47 | model: PYTORCH_MODEL MODEL=model.pt ARG=d1,d2 48 | \endplumedfile 49 | 50 | The N nodes of the neural network are saved as "model.node-0", "model.node-1", ..., "model.node-(N-1)". 51 | 52 | */ 53 | //+ENDPLUMEDOC 54 | 55 | 56 | class PytorchModel : 57 | public Function 58 | { 59 | unsigned _n_in; 60 | unsigned _n_out; 61 | torch::jit::script::Module _model; 62 | public: 63 | explicit PytorchModel(const ActionOptions&); 64 | void calculate(); 65 | static void registerKeywords(Keywords& keys); 66 | }; 67 | 68 | 69 | PLUMED_REGISTER_ACTION(PytorchModel,"PYTORCH_MODEL") 70 | 71 | void PytorchModel::registerKeywords(Keywords& keys) { 72 | Function::registerKeywords(keys); 73 | keys.use("ARG"); 74 | keys.add("optional","MODEL","filename of the trained model"); 75 | keys.addOutputComponent("node", "default", "NN outputs"); 76 | } 77 | 78 | PytorchModel::PytorchModel(const ActionOptions&ao): 79 | Action(ao), 80 | Function(ao) 81 | { 82 | //number of inputs of the model 83 | _n_in=getNumberOfArguments(); 84 | 85 | //parse model name 86 | std::string fname="model.pt"; 87 | parse("MODEL",fname); 88 | 89 | //deserialize the model from file 90 | try { 91 | _model = torch::jit::load(fname); 92 | } 93 | catch (const c10::Error& e) { 94 | error("Cannot find Pytorch model."); 95 | } 96 | 97 | checkRead(); 98 | 99 | //check the dimension of the output 100 | log.printf("Checking output dimension:\n"); 101 | std::vector input_test (_n_in); 102 | torch::Tensor single_input = torch::tensor(input_test).view({1,_n_in}); 103 | std::vector inputs; 104 | inputs.push_back( single_input ); 105 | torch::Tensor output = _model.forward( inputs ).toTensor(); 106 | vector cvs = tensor_to_vector (output); 107 | _n_out=cvs.size(); 108 | 109 | //create components 110 | for(unsigned j=0; j<_n_out; j++){ 111 | string name_comp = "node-"+std::to_string(j); 112 | addComponentWithDerivatives( name_comp ); 113 | componentIsNotPeriodic( name_comp ); 114 | } 115 | 116 | //print log 117 | //log.printf("Pytorch Model Loaded: %s \n",fname); 118 | log.printf("Number of input: %d \n",_n_in); 119 | log.printf("Number of outputs: %d \n",_n_out); 120 | 121 | } 122 | 123 | void PytorchModel::calculate() { 124 | 125 | //retrieve arguments 126 | vector current_S(_n_in); 127 | for(unsigned i=0; i<_n_in; i++) 128 | current_S[i]=getArgument(i); 129 | //convert to tensor 130 | torch::Tensor input_S = torch::tensor(current_S).view({1,_n_in}); 131 | input_S.set_requires_grad(true); 132 | //convert to Ivalue 133 | std::vector inputs; 134 | inputs.push_back( input_S ); 135 | //calculate output 136 | torch::Tensor output = _model.forward( inputs ).toTensor(); 137 | //set CV values 138 | vector cvs = tensor_to_vector (output); 139 | for(unsigned j=0; j<_n_out; j++){ 140 | string name_comp = "node-"+std::to_string(j); 141 | getPntrToComponent(name_comp)->set(cvs[j]); 142 | } 143 | //derivatives 144 | for(unsigned j=0; j<_n_out; j++){ 145 | //backpropagation 146 | output[0][j].backward(); 147 | //convert to vector 148 | vector der = tensor_to_vector (input_S.grad() ); 149 | string name_comp = "node-"+std::to_string(j); 150 | //set derivatives of component j 151 | for(unsigned i=0; i<_n_in; i++) 152 | setDerivative( getPntrToComponent(name_comp) ,i,der[i]); 153 | //reset gradients 154 | input_S.grad().zero_(); 155 | //for(unsigned i=0; i<_n_in; i++) 156 | // input_S.grad()[0][i] = 0.; 157 | 158 | } 159 | 160 | } 161 | } 162 | } 163 | --------------------------------------------------------------------------------