From 6c46bb3b701ff153de42790529327ebdc4b403dd Mon Sep 17 00:00:00 2001
From: Gareth Aneurin Tribello <garethtribello@Gareths-MacBook-Pro.local>
Date: Tue, 26 Nov 2024 17:04:13 +0000
Subject: [PATCH 1/3] Fixed secondarystructure/rt-coverage-antibetarmsd regtest
I think this regtest was maybe migrated across from version 2.9. It can't pass
if you run it in plumed 2.10 unless you make these changes.
---
.../rt-coverage-antibetarmsd/colvar.reference | 2 +-
.../rt-coverage-antibetarmsd/forces.reference | 2 +-
.../secondarystructure/rt-coverage-antibetarmsd/plumed.dat | 4 ++--
3 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/regtest/secondarystructure/rt-coverage-antibetarmsd/colvar.reference b/regtest/secondarystructure/rt-coverage-antibetarmsd/colvar.reference
index 2e093c7e02..8224042792 100644
--- a/regtest/secondarystructure/rt-coverage-antibetarmsd/colvar.reference
+++ b/regtest/secondarystructure/rt-coverage-antibetarmsd/colvar.reference
@@ -1,4 +1,4 @@
-#! FIELDS time b.lessthan brf.lessthan br.lessthan p.lessthan prf.lessthan pr.lessthan sum
+#! FIELDS time b_lessthan brf_lessthan br_lessthan p_lessthan prf_lessthan pr_lessthan sum
0.000000 0.0607 0.1654 0.1654 0.2681 0.1425 0.1425 0.3287
0.050000 0.0000 42.5600 42.5600 14.6579 4.1424 4.1424 14.6579
0.100000 0.0188 34.0262 34.0262 13.0049 3.2851 3.2851 13.0238
diff --git a/regtest/secondarystructure/rt-coverage-antibetarmsd/forces.reference b/regtest/secondarystructure/rt-coverage-antibetarmsd/forces.reference
index cbb160398c..27c89ca644 100644
--- a/regtest/secondarystructure/rt-coverage-antibetarmsd/forces.reference
+++ b/regtest/secondarystructure/rt-coverage-antibetarmsd/forces.reference
@@ -1,4 +1,4 @@
-#! FIELDS time b.lessthan brf.lessthan br.lessthan p.lessthan prf.lessthan pr.lessthan sum @8.bias @8.force2
+#! FIELDS time b_lessthan brf_lessthan br_lessthan p_lessthan prf_lessthan pr_lessthan sum r.bias r.force2
0.000000 -0.3893763023 -0.1653910914 -0.1653910914 -0.5967893540 -0.1425260828 -0.1425260828 -0.3287218854 0.0000000000 0.0000000000
0.050000 -14.6578542139 -42.5600014141 -42.5600014141 -29.3157084279 -4.1424316083 -4.1424316083 -14.6578542139 0.0000000000 0.0000000000
0.100000 -13.0426114706 -34.0261914601 -34.0261914601 -26.0287209912 -3.2850812434 -3.2850812434 -13.0237774873 0.0000000000 0.0000000000
diff --git a/regtest/secondarystructure/rt-coverage-antibetarmsd/plumed.dat b/regtest/secondarystructure/rt-coverage-antibetarmsd/plumed.dat
index 4fc2b04fd5..1985091b07 100644
--- a/regtest/secondarystructure/rt-coverage-antibetarmsd/plumed.dat
+++ b/regtest/secondarystructure/rt-coverage-antibetarmsd/plumed.dat
@@ -7,9 +7,9 @@ PARABETARMSD RESIDUES=all TYPE=OPTIMAL-FAST STRANDS_CUTOFF=1.0 LESS_THAN={RATION
PARABETARMSD RESIDUES=all TYPE=OPTIMAL STRANDS_CUTOFF=1.0 LESS_THAN={RATIONAL R_0=0.1 NN=8 MM=12 NOSTRETCH} LABEL=pr
COMBINE ARG=b.lessthan,p.lessthan PERIODIC=NO LABEL=sum
-RESTRAINT ARG=b.*,brf.*,br.*,p.*,prf.*,pr.*,sum KAPPA=1.,1.,1.,1,1,1,1 AT=0,0,0,0,0,0,0 SLOPE=0,0,0,0,0,0,0
+r: RESTRAINT ARG=b.*,brf.*,br.*,p.*,prf.*,pr.*,sum KAPPA=1.,1.,1.,1,1,1,1 AT=0,0,0,0,0,0,0 SLOPE=0,0,0,0,0,0,0
-DUMPFORCES ARG=* FILE=forces STRIDE=1
+DUMPFORCES ARG=b.*,brf.*,br.*,p.*,prf.*,pr.*,sum,r.* FILE=forces STRIDE=1
PRINT ARG=b.*,brf.*,br.*,p.*,prf.*,pr.*,sum STRIDE=1 FILE=colvar FMT=%8.4f
From 3be870e0e1ac2e950f41be1c0c3bdbdc766ac696 Mon Sep 17 00:00:00 2001
From: Gareth Aneurin Tribello <garethtribello@Gareths-MacBook-Pro.local>
Date: Tue, 26 Nov 2024 17:07:37 +0000
Subject: [PATCH 2/3] Added functionality to keep track of deprecated actions
in syntax file
---
src/cltools/GenJson.cpp | 10 ++++++++++
src/core/ActionRegister.cpp | 7 ++++---
src/multicolvar/DumpMultiColvar.cpp | 1 +
src/multicolvar/MFilterLess.cpp | 1 +
src/multicolvar/MFilterMore.cpp | 1 +
src/multicolvar/UWalls.cpp | 1 +
src/tools/Keywords.cpp | 9 +++++++++
src/tools/Keywords.h | 6 ++++++
8 files changed, 33 insertions(+), 3 deletions(-)
diff --git a/src/cltools/GenJson.cpp b/src/cltools/GenJson.cpp
index 8c9adec6ce..44ae7ced84 100644
--- a/src/cltools/GenJson.cpp
+++ b/src/cltools/GenJson.cpp
@@ -123,6 +123,16 @@ int GenJson::main(FILE* in, FILE*out,Communicator& pc) {
// Now output keyword information
Keywords keys; actionRegister().getKeywords( action_names[i], keys );
std::cout<<" \"displayname\" : \""<<keys.getDisplayName()<<"\",\n";
+ // This is used for noting actions that have been deprecated
+ std::string replacement = keys.getReplacementAction();
+ if( replacement!="none" ) {
+ bool found=false;
+ for(unsigned j=0; j<action_names.size(); ++j) {
+ if( action_names[j]==replacement ) { found=true; break; }
+ }
+ if( !found ) error("could not find action named " + replacement + " that is supposed to be used to replace " + action_names[i] );
+ }
+ std::cout<<" \"replacement\" : \""<<replacement<<"\",\n";
std::cout<<" \"syntax\" : {"<<std::endl;
for(unsigned j=0; j<keys.size(); ++j) {
std::string defa = "", desc = keys.getKeywordDescription( keys.getKeyword(j) );
diff --git a/src/core/ActionRegister.cpp b/src/core/ActionRegister.cpp
index 616a1cafe8..f204cfa99d 100644
--- a/src/core/ActionRegister.cpp
+++ b/src/core/ActionRegister.cpp
@@ -41,7 +41,7 @@ std::unique_ptr<Action> ActionRegister::create(const std::vector<void*> & images
auto content=get(images,ao.line[0]);
Keywords keys; keys.thisactname = ao.line[0];
- content.keys(keys);
+ keys.replaceaction = "none"; content.keys(keys);
ActionOptions nao( ao,keys );
auto fullPath=getFullPath(images,ao.line[0]);
nao.setFullPath(fullPath);
@@ -79,7 +79,7 @@ bool ActionRegister::printTemplate(const std::string& action, bool include_optio
//no need to insert the try/catch block: check will ensure that action is known
if( check(action) ) {
Keywords keys; keys.thisactname = action;
- get(action).keys(keys);
+ keys.replaceaction = "none"; get(action).keys(keys);
keys.print_template(action, include_optional);
return true;
} else {
@@ -101,6 +101,7 @@ bool ActionRegister::getKeywords(const std::string& action, Keywords& keys) {
//no need to insert the try/catch block: check will ensure that action is known
if(check(action)) {
keys.thisactname = action;
+ keys.replaceaction = "none";
get(action).keys(keys);
return true;
}
@@ -108,7 +109,7 @@ bool ActionRegister::getKeywords(const std::string& action, Keywords& keys) {
}
void ActionRegister::getKeywords(const std::vector<void*> & images, const std::string& action, Keywords& keys) {
- auto content=get(images,action); keys.thisactname = action; content.keys(keys);
+ auto content=get(images,action); keys.thisactname = action; keys.replaceaction = "none"; content.keys(keys);
}
}
diff --git a/src/multicolvar/DumpMultiColvar.cpp b/src/multicolvar/DumpMultiColvar.cpp
index b716a99cef..a0b04d25d8 100644
--- a/src/multicolvar/DumpMultiColvar.cpp
+++ b/src/multicolvar/DumpMultiColvar.cpp
@@ -47,6 +47,7 @@ PLUMED_REGISTER_ACTION(DumpMultiColvar,"DUMPMULTICOLVAR")
void DumpMultiColvar::registerKeywords(Keywords& keys) {
ActionShortcut::registerKeywords( keys );
+ keys.setDeprecated("DUMPATOMS");
keys.add("compulsory","DATA","the vector you wish to transform");
keys.add("compulsory","FILE","the file that you would like to output the data to");
keys.remove("HAS_VALUES"); keys.needsAction("DUMPATOMS");
diff --git a/src/multicolvar/MFilterLess.cpp b/src/multicolvar/MFilterLess.cpp
index 83f1978515..b8f0c817f3 100644
--- a/src/multicolvar/MFilterLess.cpp
+++ b/src/multicolvar/MFilterLess.cpp
@@ -47,6 +47,7 @@ PLUMED_REGISTER_ACTION(MFilterLess,"MFILTER_LESS")
void MFilterLess::registerKeywords(Keywords& keys) {
ActionShortcut::registerKeywords( keys );
+ keys.setDeprecated("LESS_THAN");
keys.add("compulsory","DATA","the vector you wish to transform");
keys.add("compulsory","SWITCH","the switching function that transform");
keys.setValueDescription("vector","a vector that has the same dimension as the input vector with elements equal to one if the corresponding component of the vector is less than a tolerance and zero otherwise");
diff --git a/src/multicolvar/MFilterMore.cpp b/src/multicolvar/MFilterMore.cpp
index 363a773891..2507d1b3a8 100644
--- a/src/multicolvar/MFilterMore.cpp
+++ b/src/multicolvar/MFilterMore.cpp
@@ -47,6 +47,7 @@ PLUMED_REGISTER_ACTION(MFilterMore,"MFILTER_MORE")
void MFilterMore::registerKeywords(Keywords& keys) {
ActionShortcut::registerKeywords( keys );
+ keys.setDeprecated("MORE_THAN");
keys.add("compulsory","DATA","the vector you wish to transform");
keys.add("compulsory","SWITCH","the switching function that transform");
keys.addFlag("LOWMEM",false,"this flag does nothing and is present only to ensure back-compatibility");
diff --git a/src/multicolvar/UWalls.cpp b/src/multicolvar/UWalls.cpp
index 68892cdf57..29d6dffd61 100644
--- a/src/multicolvar/UWalls.cpp
+++ b/src/multicolvar/UWalls.cpp
@@ -48,6 +48,7 @@ PLUMED_REGISTER_ACTION(UWalls,"UWALLS")
void UWalls::registerKeywords(Keywords& keys) {
ActionShortcut::registerKeywords( keys );
+ keys.setDeprecated("UPPER_WALLS");
keys.add("compulsory","DATA","the values you want to restrain");
keys.add("compulsory","AT","the radius of the sphere");
keys.add("compulsory","KAPPA","the force constant for the wall. The k_i in the expression for a wall.");
diff --git a/src/tools/Keywords.cpp b/src/tools/Keywords.cpp
index ca9af95d6e..4904a0ccd8 100644
--- a/src/tools/Keywords.cpp
+++ b/src/tools/Keywords.cpp
@@ -776,4 +776,13 @@ std::string Keywords::getDisplayName() const {
return thisactname;
}
+void Keywords::setDeprecated( const std::string& name ) {
+ replaceaction = name;
+}
+
+std::string Keywords::getReplacementAction() const {
+ return replaceaction;
+}
+
+
}
diff --git a/src/tools/Keywords.h b/src/tools/Keywords.h
index efce8b38a0..6c84a5a601 100644
--- a/src/tools/Keywords.h
+++ b/src/tools/Keywords.h
@@ -66,6 +66,8 @@ class Keywords {
bool isatoms;
/// The name of the action that has this set of keywords
std::string thisactname;
+/// The action to use in place of this deprecated action
+ std::string replaceaction;
/// The names of the allowed keywords
std::vector<std::string> keys;
/// The names of the reserved keywords
@@ -217,6 +219,10 @@ class Keywords {
std::string getDisplayName() const ;
/// Set the display name
void setDisplayName( const std::string& name );
+/// Get the action that should be used to replace this one if action has been deprecated
+ std::string getReplacementAction() const ;
+/// Note that this action has been deprecated
+ void setDeprecated( const std::string& name );
};
}
From 347fc5063aac303abc9a0042837855a7541c4d87 Mon Sep 17 00:00:00 2001
From: Gareth Aneurin Tribello <garethtribello@Gareths-MacBook-Pro.local>
Date: Tue, 26 Nov 2024 17:12:01 +0000
Subject: [PATCH 3/3] Ran astyle
---
src/cltools/GenJson.cpp | 10 +++++-----
src/tools/Keywords.cpp | 2 +-
2 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/src/cltools/GenJson.cpp b/src/cltools/GenJson.cpp
index 44ae7ced84..bd609eb880 100644
--- a/src/cltools/GenJson.cpp
+++ b/src/cltools/GenJson.cpp
@@ -126,11 +126,11 @@ int GenJson::main(FILE* in, FILE*out,Communicator& pc) {
// This is used for noting actions that have been deprecated
std::string replacement = keys.getReplacementAction();
if( replacement!="none" ) {
- bool found=false;
- for(unsigned j=0; j<action_names.size(); ++j) {
- if( action_names[j]==replacement ) { found=true; break; }
- }
- if( !found ) error("could not find action named " + replacement + " that is supposed to be used to replace " + action_names[i] );
+ bool found=false;
+ for(unsigned j=0; j<action_names.size(); ++j) {
+ if( action_names[j]==replacement ) { found=true; break; }
+ }
+ if( !found ) error("could not find action named " + replacement + " that is supposed to be used to replace " + action_names[i] );
}
std::cout<<" \"replacement\" : \""<<replacement<<"\",\n";
std::cout<<" \"syntax\" : {"<<std::endl;
diff --git a/src/tools/Keywords.cpp b/src/tools/Keywords.cpp
index 4904a0ccd8..231993b371 100644
--- a/src/tools/Keywords.cpp
+++ b/src/tools/Keywords.cpp
@@ -782,7 +782,7 @@ void Keywords::setDeprecated( const std::string& name ) {
std::string Keywords::getReplacementAction() const {
return replaceaction;
-}
+}
}