Merge branch 'v2.10'

plumed · Jan 16, 2025 · dd87c04 · dd87c04 · PlumedBot · Jan 16, 2025
2 parents a43124e + 57fddfe
commit dd87c04
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Showing 23 changed files with 31 additions and 28 deletions.
diff --git a/regtest/basic/rt-cregex-backward-compatibility/Makefile b/regtest/basic/rt-cregex-backward-compatibility/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/basic/rt-cregex-backward-compatibility/config b/regtest/basic/rt-cregex-backward-compatibility/config
@@ -0,0 +1,3 @@
+type=plumed
+#this just tests that config will always return cregex as existing, for backward compatibility
+arg="config has cregex"
diff --git a/regtest/basic/rt-cregex-backward-compatibility/out.reference b/regtest/basic/rt-cregex-backward-compatibility/out.reference
@@ -0,0 +1 @@
+cregex on
diff --git a/regtest/isdb/rt-Metainference-averaging/config b/regtest/isdb/rt-Metainference-averaging/config
@@ -1,4 +1,3 @@
-plumed_needs="cregex"
 type=driver
 # this is to test a different name
 arg="--plumed plumed.dat --trajectory-stride 2 --timestep 0.002 --mf_xtc trajectory.xtc --dump-forces atom_forces --dump-forces-fmt=%7.3f"
diff --git a/regtest/isdb/rt-jcoupling-string-type/config b/regtest/isdb/rt-jcoupling-string-type/config
@@ -1,4 +1,3 @@
-plumed_needs="cregex"
 type=driver
 # this is to test a different name
 arg="--plumed plumed.dat --trajectory-stride 2 --timestep 0.002 --mf_xtc trajectory.xtc --dump-forces atom_forces --dump-forces-fmt=%7.3f"
diff --git a/regtest/isdb/rt-metainference-mc-chunksize/config b/regtest/isdb/rt-metainference-mc-chunksize/config
@@ -1,4 +1,3 @@
-plumed_needs="cregex"
 type=driver
 # this is to test a different name
 arg="--plumed plumed.dat --trajectory-stride 2 --timestep 0.002 --mf_xtc trajectory.xtc --dump-forces atom_forces --dump-forces-fmt=%7.3f"
diff --git a/regtest/isdb/rt-metainference-optisigmamean-sem-max/config b/regtest/isdb/rt-metainference-optisigmamean-sem-max/config
@@ -1,4 +1,3 @@
-plumed_needs="cregex"
 type=driver
 # this is to test a different name
 arg="--plumed plumed.dat --trajectory-stride 2 --timestep 0.002 --mf_xtc trajectory.xtc --dump-forces atom_forces --dump-forces-fmt=%7.3f"
diff --git a/regtest/isdb/rt-metainference-optisigmamean-sem/config b/regtest/isdb/rt-metainference-optisigmamean-sem/config
@@ -1,4 +1,3 @@
-plumed_needs="cregex"
 type=driver
 # this is to test a different name
 arg="--plumed plumed.dat --trajectory-stride 2 --timestep 0.002 --mf_xtc trajectory.xtc --dump-forces atom_forces --dump-forces-fmt=%7.3f"
diff --git a/regtest/isdb/rt-metainference-regres-zero/MISTATUSmij.reference b/regtest/isdb/rt-metainference-regres-zero/MISTATUSmij.reference
@@ -1,2 +1,2 @@
 #! FIELDS time sigmaMean_0_0 sigma_0 sigma_max_0 scale0_ offset0_ weight_0
-                      0                     10                      1                     10       1.13019842568893                      0                      1
+   0.0000000  10.0000000   1.0000000  10.0000000   1.1301984   0.0000000   1.0000000
diff --git a/regtest/isdb/rt-metainference-regres-zero/config b/regtest/isdb/rt-metainference-regres-zero/config
@@ -1,4 +1,3 @@
-plumed_needs="cregex"
 type=driver
 # this is to test a different name
 arg="--plumed plumed.dat --trajectory-stride 2 --timestep 0.002 --mf_xtc trajectory.xtc --dump-forces atom_forces --dump-forces-fmt=%7.3f"
diff --git a/regtest/isdb/rt-metainference-regres-zero/plumed.dat b/regtest/isdb/rt-metainference-regres-zero/plumed.dat
@@ -24,6 +24,7 @@ DSIGMA=0
 LABEL=mij
 TEMP=300
 REGRES_ZERO=1
+FMT=%12.7lf
 ...
 
 JCOUPLING ...
@@ -43,6 +44,7 @@ JCOUPLING ...
     DSIGMA=0
     TEMP=300
     RESTART=YES
+    FMT=%12.7lf
 ... JCOUPLING
 
 BIASVALUE ARG=jmi.score

diff --git a/regtest/isdb/rt-metainferencebase-averaging/config b/regtest/isdb/rt-metainferencebase-averaging/config
@@ -1,4 +1,3 @@
-plumed_needs="cregex"
 type=driver
 # this is to test a different name
 arg="--plumed plumed.dat --trajectory-stride 2 --timestep 0.002 --mf_xtc trajectory.xtc --dump-forces atom_forces --dump-forces-fmt=%7.3f"
diff --git a/regtest/isdb/rt-metainferencebase-regres-zero/config b/regtest/isdb/rt-metainferencebase-regres-zero/config
@@ -1,4 +1,3 @@
-plumed_needs="cregex"
 type=driver
 
 arg="--plumed plumed.dat --trajectory-stride 2 --timestep 0.002 --mf_xtc trajectory.xtc --dump-forces atom_forces --dump-forces-fmt=%7.3f"
diff --git a/regtest/isdb/rt-metainferencebase-sem-max/config b/regtest/isdb/rt-metainferencebase-sem-max/config
@@ -1,4 +1,3 @@
-plumed_needs="cregex"
 type=driver
 # this is to test a different name
 arg="--plumed plumed.dat --trajectory-stride 2 --timestep 0.002 --mf_xtc trajectory.xtc --dump-forces atom_forces --dump-forces-fmt=%7.3f"
diff --git 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
@@ -1,7 +1,7 @@
-#! FIELDS time b.lessthan brf.lessthan br.lessthan p.lessthan prf.lessthan pr.lessthan sum @8.bias @8.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
- 0.150000  -16.2009073956  -47.7585572573  -47.7585572573  -32.4018147912   -4.3920871588   -4.3920871588  -16.2009073956    0.0000000000    0.0000000000
- 0.200000  -57.6661791916   -2.2688460225   -2.2688460225 -115.3323583831  -45.9215920978  -45.9215920978  -57.6661791916    0.0000000000    0.0000000000
- 0.250000 -100.7083276804   -4.8852734198   -4.8852734198 -201.4166553607  -83.4591661722  -83.4591661722 -100.7083276804    0.0000000000    0.0000000000
+#! FIELDS time b_lessthan brf_lessthan br_lessthan p_lessthan prf_lessthan pr_lessthan sum
+ 0.000000   -0.3893763023   -0.1653910914   -0.1653910914   -0.5967893540   -0.1425260828   -0.1425260828   -0.3287218854
+ 0.050000  -14.6578542139  -42.5600014141  -42.5600014141  -29.3157084279   -4.1424316083   -4.1424316083  -14.6578542139
+ 0.100000  -13.0426114706  -34.0261914601  -34.0261914601  -26.0287209912   -3.2850812434   -3.2850812434  -13.0237774873
+ 0.150000  -16.2009073956  -47.7585572573  -47.7585572573  -32.4018147912   -4.3920871588   -4.3920871588  -16.2009073956
+ 0.200000  -57.6661791916   -2.2688460225   -2.2688460225 -115.3323583831  -45.9215920978  -45.9215920978  -57.6661791916
+ 0.250000 -100.7083276804   -4.8852734198   -4.8852734198 -201.4166553607  -83.4591661722  -83.4591661722 -100.7083276804
diff --git a/regtest/secondarystructure/rt-coverage-antibetarmsd/plumed.dat b/regtest/secondarystructure/rt-coverage-antibetarmsd/plumed.dat
@@ -9,7 +9,7 @@ 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
 
-DUMPFORCES ARG=* FILE=forces STRIDE=1
+DUMPFORCES ARG=b.*,brf.*,br.*,p.*,prf.*,pr.*,sum FILE=forces STRIDE=1
 
 PRINT ARG=b.*,brf.*,br.*,p.*,prf.*,pr.*,sum STRIDE=1 FILE=colvar FMT=%8.4f
 
diff --git a/src/config/Config.h b/src/config/Config.h
@@ -99,7 +99,8 @@ bool hasDlopen();
 
 bool isInstalled();
 
-bool hasCregex();
+/// This will always return true for backward compatibility
+constexpr bool hasCregex() {return true;}
 
 bool hasMolfile();
 

diff --git a/src/config/Config.inc.in b/src/config/Config.inc.in
@@ -155,14 +155,6 @@ bool hasDlopen() {
 #endif
 }
 
-bool hasCregex() {
-#ifdef __PLUMED_HAS_CREGEX
-  return true;
-#else
-  return false;
-#endif
-}
-
 bool hasMolfile() {
 #ifdef __PLUMED_HAS_MOLFILE_PLUGINS
   return true;

diff --git a/src/isdb/Metainference.cpp b/src/isdb/Metainference.cpp
@@ -318,6 +318,7 @@ void Metainference::registerKeywords(Keywords& keys) {
   keys.add("optional","MC_STEPS","number of MC steps");
   keys.add("optional","MC_CHUNKSIZE","MC chunksize");
   keys.add("optional","STATUS_FILE","write a file with all the data useful for restart/continuation of Metainference");
+  keys.add("optional","FMT","specify format for HILLS files (useful for decrease the number of digits in regtests)");
   keys.add("compulsory","WRITE_STRIDE","10000","write the status to a file every N steps, this can be used for restart/continuation");
   keys.add("optional","SELECTOR","name of selector");
   keys.add("optional","NSELECT","range of values for selector [0, N-1]");
@@ -590,6 +591,9 @@ Metainference::Metainference(const ActionOptions&ao):
     /* in this case Dsigma is initialised after reading the restart file if present */
   }
 
+  std::string fmt_;
+  parse("FMT",fmt_);
+
   // monte carlo stuff
   parse("MC_STEPS",MCsteps_);
   parse("MC_CHUNKSIZE", MCchunksize_);
@@ -901,6 +905,7 @@ Metainference::Metainference(const ActionOptions&ao):
   if(write_stride_>0) {
     sfile_.link(*this);
     sfile_.open(status_file_name_);
+    if(fmt_.length()>0) sfile_.fmtField(fmt_);
   }
 
   log<<"  Bibliography "<<plumed.cite("Bonomi, Camilloni, Cavalli, Vendruscolo, Sci. Adv. 2, e150117 (2016)");

diff --git a/src/isdb/MetainferenceBase.cpp b/src/isdb/MetainferenceBase.cpp
@@ -68,6 +68,7 @@ void MetainferenceBase::registerKeywords( Keywords& keys ) {
   keys.add("optional","MC_STEPS","number of MC steps");
   keys.add("optional","MC_CHUNKSIZE","MC chunksize");
   keys.add("optional","STATUS_FILE","write a file with all the data useful for restart/continuation of Metainference");
+  keys.add("optional","FMT","specify format for HILLS files (useful for decrease the number of digits in regtests)");
   keys.add("compulsory","WRITE_STRIDE","10000","write the status to a file every N steps, this can be used for restart/continuation");
   keys.add("optional","SELECTOR","name of selector");
   keys.add("optional","NSELECT","range of values for selector [0, N-1]");
@@ -317,6 +318,8 @@ MetainferenceBase::MetainferenceBase(const ActionOptions&ao):
     /* in this case Dsigma is initialised after reading the restart file if present */
   }
 
+  parse("FMT",fmt_);
+
   // monte carlo stuff
   parse("MC_STEPS",MCsteps_);
   parse("MC_CHUNKSIZE", MCchunksize_);
@@ -359,6 +362,7 @@ MetainferenceBase::MetainferenceBase(const ActionOptions&ao):
   if(write_stride_>0&&doscore_) {
     sfile_.link(*this);
     sfile_.open(status_file_name_);
+    if(fmt_.length()>0) sfile_.fmtField(fmt_);
   }
 
 }

diff --git a/src/isdb/MetainferenceBase.h b/src/isdb/MetainferenceBase.h
@@ -124,6 +124,7 @@ class MetainferenceBase :
   // restart
   std::string status_file_name_;
   OFile    sfile_;
+  std::string fmt_;
 
   // others
   bool     firstTime;

diff --git a/src/maketools/update-config-txt.sh b/src/maketools/update-config-txt.sh
@@ -132,6 +132,8 @@ echo "# if option xx is on then plumed has beeen compiled with -D__PLUMED_HAS_XX
       echo "has $u off"
     fi
   done
+  #this is here for backward compatibility (since we are using c++17 that has <regex>)
+  echo "has cregex on"
 } | sort
 echo
 echo "# other defines"