From 7c2fbaaa6ca7ee8d0a963adb6ec9b67be73886d6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= <heninj@gmail.com>
Date: Tue, 28 May 2024 16:42:14 +0200
Subject: [PATCH] Move AMBD ref to other bibtex file, fix typos

and assorted small fixes thanks to code review by Giacomo
---
 doc/colvars-code-refs.bib | 14 +-------------
 doc/colvars-refman.bib    | 12 ++++++++++++
 src/colvarbias_abmd.cpp   |  2 +-
 src/colvarbias_abmd.h     |  3 +--
 src/colvarmodule_refs.h   | 22 +++-------------------
 5 files changed, 18 insertions(+), 35 deletions(-)

diff --git a/doc/colvars-code-refs.bib b/doc/colvars-code-refs.bib
index 81b2d2dbb..e953097a4 100644
--- a/doc/colvars-code-refs.bib
+++ b/doc/colvars-code-refs.bib
@@ -329,19 +329,6 @@ @article{White2014
   url = {https://doi.org/10.1021/ct500320c}
 }
 
-% ABMD bias
-@Article{Marchi1999,
-  author  = {Massimo Marchi and Pietro Ballone},
-  journal = {J. Chem. Phys.},
-  title   = {Adiabatic bias molecular dynamics: A method to navigate the conformational space of complex molecular systems},
-  year    = {1999},
-  number  = {8},
-  pages   = {3697-3702},
-  volume  = {110},
-  doi     = {10.1063/1.478259},
-  url     = {https://doi.org/10.1063/1.478259},
-}
-
 
 % --- NO CITATIONS AVAILABLE YET FOR THESE FEATURES ---
 % Colvars-GROMACS interface
@@ -355,4 +342,5 @@ @Article{Marchi1999
 % coordNum pairlist
 % Custom functions (Lepton)
 % Scripted functions (Tcl)
+% ABMD bias
 % --- END ---
diff --git a/doc/colvars-refman.bib b/doc/colvars-refman.bib
index 72a7d144d..9ca858816 100644
--- a/doc/colvars-refman.bib
+++ b/doc/colvars-refman.bib
@@ -234,6 +234,18 @@ @ARTICLE{Leines2012
     pages = {020601},
 }
 
+@Article{Marchi1999,
+  author  = {Massimo Marchi and Pietro Ballone},
+  journal = {J. Chem. Phys.},
+  title   = {Adiabatic bias molecular dynamics: A method to navigate the conformational space of complex molecular systems},
+  year    = {1999},
+  number  = {8},
+  pages   = {3697-3702},
+  volume  = {110},
+  doi     = {10.1063/1.478259},
+  url     = {https://doi.org/10.1063/1.478259},
+}
+
 @ARTICLE{Marinelli2009,
   author = {Marinelli, Fabrizio AND Pietrucci, Fabio AND Laio, Alessandro AND Piana, Stefano},
   journal = {PLOS Computational Biology},
diff --git a/src/colvarbias_abmd.cpp b/src/colvarbias_abmd.cpp
index e6a6ed15d..4825c73be 100644
--- a/src/colvarbias_abmd.cpp
+++ b/src/colvarbias_abmd.cpp
@@ -120,7 +120,7 @@ std::ostream & colvarbias_abmd::write_traj_label(std::ostream &os)
 {
   size_t const this_cv_width = (variables(0)->value()).output_width(cvm::cv_width);
   os << " ref_"
-      << cvm::wrap_string(variables(0)->name, this_cv_width-3);
+      << cvm::wrap_string(variables(0)->name, this_cv_width-4);
 
   return os;
 }
diff --git a/src/colvarbias_abmd.h b/src/colvarbias_abmd.h
index 2ce736297..96278c2de 100644
--- a/src/colvarbias_abmd.h
+++ b/src/colvarbias_abmd.h
@@ -13,8 +13,7 @@
 #include "colvarbias_restraint.h"
 
 
-/// \brief Wall restraint
-/// (implementation of \link colvarbias_restraint \endlink)
+/// \brief Adiabatic Bias MD
 class colvarbias_abmd
   : public colvarbias_ti
 {
diff --git a/src/colvarmodule_refs.h b/src/colvarmodule_refs.h
index 9e3092866..2e9615e3b 100644
--- a/src/colvarmodule_refs.h
+++ b/src/colvarmodule_refs.h
@@ -344,22 +344,6 @@
     "  url = {https://doi.org/10.1021/ct500320c}\n"
     "}\n";
 
-  paper_count_[std::string("Marchi1999")] = 0;
-  paper_url_[std::string("Marchi1999")] = "https://doi.org/10.1063/1.478259";
-  paper_bibtex_[std::string("Marchi1999")] =
-    "\n"
-    "@Article{Marchi1999,\n"
-    "  author  = {Massimo Marchi and Pietro Ballone},\n"
-    "  journal = {J. Chem. Phys.},\n"
-    "  title   = {Adiabatic bias molecular dynamics: A method to navigate the conformational space of complex molecular systems},\n"
-    "  year    = {1999},\n"
-    "  number  = {8},\n"
-    "  pages   = {3697-3702},\n"
-    "  volume  = {110},\n"
-    "  doi     = {10.1063/1.478259},\n"
-    "  url     = {https://doi.org/10.1063/1.478259},\n"
-    "}\n";
-
   paper_count_[std::string("n/a")] = 0;
   paper_url_[std::string("n/a")] = "";
   paper_bibtex_[std::string("n/a")] = "";
@@ -571,9 +555,6 @@
   feature_count_[std::string("ALB colvar bias implementation")] = 0;
   feature_paper_map_[std::string("ALB colvar bias implementation")] = "White2014";
 
-  feature_count_[std::string("ABMD bias")] = 0;
-  feature_paper_map_[std::string("ABMD bias")] = "Marchi1999";
-
   feature_count_[std::string("Colvars-GROMACS interface")] = 0;
   feature_paper_map_[std::string("Colvars-GROMACS interface")] = "n/a";
 
@@ -606,3 +587,6 @@
 
   feature_count_[std::string("Scripted functions (Tcl)")] = 0;
   feature_paper_map_[std::string("Scripted functions (Tcl)")] = "n/a";
+
+  feature_count_[std::string("ABMD bias")] = 0;
+  feature_paper_map_[std::string("ABMD bias")] = "n/a";