diff --git a/doc/colvars-code-refs.bib b/doc/colvars-code-refs.bib index 0a1a0d811..84cfa1be8 100644 --- a/doc/colvars-code-refs.bib +++ b/doc/colvars-code-refs.bib @@ -144,6 +144,17 @@ @article{Fiorin2020 url = {https://doi.org/10.1002/jcc.26075} } +% Colvars-GROMACS interface +% gspath colvar component +% gzpath colvar component +% linearCombination colvar component +% gspathCV colvar component +% gzpathCV colvar component +% aspathCV colvar component +% azpathCV colvar component +% Custom functions (Lepton) +% Scripted functions (Tcl) +% ABMD bias % Updated multiple-walker ABF implementation @article{Fiorin2024, author = {Fiorin, Giacomo and Marinelli, Fabrizio and Forrest, Lucy R. and Chen, Haochuan and Chipot, Christophe and Kohlmeyer, Axel and Santuz, Hubert and H{\'e}nin, J{\'e}rôme}, @@ -376,19 +387,7 @@ @article{Invernizzi2022 pages = {3988--3996}, } - % --- NO CITATIONS AVAILABLE YET FOR THESE FEATURES --- -% Colvars-GROMACS interface -% gspath colvar component -% gzpath colvar component -% linearCombination colvar component -% gspathCV colvar component -% gzpathCV colvar component -% aspathCV colvar component -% azpathCV colvar component % coordNum pairlist -% Custom functions (Lepton) -% Scripted functions (Tcl) -% torchANN colvar component -% ABMD bias +% torchANN colvar component % --- END --- diff --git a/src/colvarmodule_refs.h b/src/colvarmodule_refs.h index fa702a0a7..7af4656e6 100644 --- a/src/colvarmodule_refs.h +++ b/src/colvarmodule_refs.h @@ -137,9 +137,9 @@ " author = {Fiorin, Giacomo and Marinelli, Fabrizio and Forrest, Lucy R. and Chen, Haochuan and Chipot, Christophe and Kohlmeyer, Axel and Santuz, Hubert and H{\\'e}nin, J{\\'e}rôme},\n" " title = {Expanded Functionality and Portability for the Colvars Library},\n" " journal = {J. Phys. Chem. {B}},\n" - " volume = {0},\n" - " number = {0},\n" - " pages = {null},\n" + " volume = {128},\n" + " number = {45},\n" + " pages = {11108--11123},\n" " year = {2024},\n" " doi = {10.1021/acs.jpcb.4c05604},\n" " pmid = 39501453,\n" @@ -545,6 +545,39 @@ feature_count_[std::string("Multi-Map collective variables")] = 0; feature_paper_map_[std::string("Multi-Map collective variables")] = "Fiorin2020"; + feature_count_[std::string("Colvars-GROMACS interface")] = 0; + feature_paper_map_[std::string("Colvars-GROMACS interface")] = "Fiorin2024"; + + feature_count_[std::string("gspath colvar component")] = 0; + feature_paper_map_[std::string("gspath colvar component")] = "Fiorin2024"; + + feature_count_[std::string("gzpath colvar component")] = 0; + feature_paper_map_[std::string("gzpath colvar component")] = "Fiorin2024"; + + feature_count_[std::string("linearCombination colvar component")] = 0; + feature_paper_map_[std::string("linearCombination colvar component")] = "Fiorin2024"; + + feature_count_[std::string("gspathCV colvar component")] = 0; + feature_paper_map_[std::string("gspathCV colvar component")] = "Fiorin2024"; + + feature_count_[std::string("gzpathCV colvar component")] = 0; + feature_paper_map_[std::string("gzpathCV colvar component")] = "Fiorin2024"; + + feature_count_[std::string("aspathCV colvar component")] = 0; + feature_paper_map_[std::string("aspathCV colvar component")] = "Fiorin2024"; + + feature_count_[std::string("azpathCV colvar component")] = 0; + feature_paper_map_[std::string("azpathCV colvar component")] = "Fiorin2024"; + + feature_count_[std::string("Custom functions (Lepton)")] = 0; + feature_paper_map_[std::string("Custom functions (Lepton)")] = "Fiorin2024"; + + feature_count_[std::string("Scripted functions (Tcl)")] = 0; + feature_paper_map_[std::string("Scripted functions (Tcl)")] = "Fiorin2024"; + + feature_count_[std::string("ABMD bias")] = 0; + feature_paper_map_[std::string("ABMD bias")] = "Fiorin2024"; + feature_count_[std::string("Updated multiple-walker ABF implementation")] = 0; feature_paper_map_[std::string("Updated multiple-walker ABF implementation")] = "Fiorin2024"; @@ -620,41 +653,8 @@ feature_count_[std::string("OPES explore or adaptive kernels")] = 0; feature_paper_map_[std::string("OPES explore or adaptive kernels")] = "Invernizzi2022"; - feature_count_[std::string("Colvars-GROMACS interface")] = 0; - feature_paper_map_[std::string("Colvars-GROMACS interface")] = "n/a"; - - feature_count_[std::string("gspath colvar component")] = 0; - feature_paper_map_[std::string("gspath colvar component")] = "n/a"; - - feature_count_[std::string("gzpath colvar component")] = 0; - feature_paper_map_[std::string("gzpath colvar component")] = "n/a"; - - feature_count_[std::string("linearCombination colvar component")] = 0; - feature_paper_map_[std::string("linearCombination colvar component")] = "n/a"; - - feature_count_[std::string("gspathCV colvar component")] = 0; - feature_paper_map_[std::string("gspathCV colvar component")] = "n/a"; - - feature_count_[std::string("gzpathCV colvar component")] = 0; - feature_paper_map_[std::string("gzpathCV colvar component")] = "n/a"; - - feature_count_[std::string("aspathCV colvar component")] = 0; - feature_paper_map_[std::string("aspathCV colvar component")] = "n/a"; - - feature_count_[std::string("azpathCV colvar component")] = 0; - feature_paper_map_[std::string("azpathCV colvar component")] = "n/a"; - feature_count_[std::string("coordNum pairlist")] = 0; feature_paper_map_[std::string("coordNum pairlist")] = "n/a"; - feature_count_[std::string("Custom functions (Lepton)")] = 0; - feature_paper_map_[std::string("Custom functions (Lepton)")] = "n/a"; - - feature_count_[std::string("Scripted functions (Tcl)")] = 0; - feature_paper_map_[std::string("Scripted functions (Tcl)")] = "n/a"; - feature_count_[std::string("torchANN colvar component")] = 0; feature_paper_map_[std::string("torchANN colvar component")] = "n/a"; - - feature_count_[std::string("ABMD bias")] = 0; - feature_paper_map_[std::string("ABMD bias")] = "n/a";