Add references to new Colvars paper

README.md

@@ -25,11 +25,12 @@ To reflect the different availability of features in each engine, the Colvars re
 
 ## Citing
 
-The reference article is:
-G. Fiorin, M. L. Klein, and J. Hénin, Mol. Phys. **111** (22-23), 3345-3362 (2013).
-https://doi.org/10.1080/00268976.2013.813594  \[[BibTex file](https://github.com/Colvars/colvars/blob/master/doc/ref_Fiorin_2013.bib?raw=true)\] \[[Endnote file](https://github.com/Colvars/colvars/blob/master/doc/ref_Fiorin_2013.ciw?raw=true)\]
+Please cite the following papers when using the library:
 
-*Additional references for the implementation of specific features are listed in the [documentation](#documentation).*  Beginning with Colvars 2021-08-30, these references, including acknowledgments of specific code from the MD engine, are also printed to the screen/logfile when they are used.
+- G. Fiorin, M. L. Klein, and J. Hénin, Mol. Phys. **111** (22-23), 3345-3362 (2013).  https://doi.org/10.1080/00268976.2013.813594
+- G. Fiorin, F. Marinelli, L. R. Forrest, H. Chen, C. Chipot, A. Kohlmeyer, H. Santuz, J. Hénin, J. Phys. Chem. B **128** (45), 11108-11123 (2024).  https://doi.org/10.1021/acs.jpcb.4c05604
+
+*References to specific code features* are also listed in the [documentation](#documentation) and printed at runtime when their features are used.  A [BibTex file](https://github.com/Colvars/colvars/blob/master/doc/colvars-code-refs.bib?raw=true) containing all of these is also available.
 
 *Note to NAMD users:* the NAMD reference papers (Phillips *et al*, [2005](https://doi.org/10.1002/jcc.20289) and [2020](https://doi.org/10.1063/5.0014475)) are used in some publications to acknowledge Colvars features.  This is incomplete.  When possible, please consider identifying and acknowledging all development efforts that supported your project.  As an important clarification, most of the Colvars code was developed *outside* of the NAMD/VMD funding grants.
 

doc/colvars-code-refs.bib

@@ -144,14 +144,25 @@ @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},
   title = {Expanded Functionality and Portability for the Colvars Library},
   journal = {J. Phys. Chem. {B}},
-  volume = {0},
-  number = {0},
-  pages = {null},
+  volume = {128},
+  number = {45},
+  pages = {11108--11123},
   year = {2024},
   doi = {10.1021/acs.jpcb.4c05604},
   pmid = 39501453,
@@ -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 ---

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";