Moved all pamm stuff to separate module

regtest/.gitignore

@@ -16,6 +16,7 @@
 !/manyrestraints
 !/molfile_plugin
 !/has-almost
+!/pamm
 # These files we just want to ignore completely
 tmp
 report.txt

regtest/pamm/Makefile

+include ../scripts/module.make
+

regtest/adjmat/rt-hbpamm/plumed.dat → regtest/pamm/rt-hbpamm/plumed.dat

-mat: HBPAMM ATOMS=1-192:3 CLUSTERS=b3lyp.pamm HYDROGENS=2-192:3,3-192:3 SUM
+mat: HBPAMM_MATRIX ATOMS=1-192:3 CLUSTERS=b3lyp.pamm HYDROGENS=2-192:3,3-192:3 SUM
 
 ROWSUMS MATRIX=mat MEAN LABEL=rsums
 COLUMNSUMS MATRIX=mat MEAN LABEL=csums
@@ -8,17 +8,17 @@ DUMPMULTICOLVAR DATA=csums PRECISION=4 FILE=acceptors.xyz
 
 PRINT ARG=rsums.*,csums.* FILE=colvar FMT=%8.4f
 
-hbo: HBPAMM_PERH SITES=1-192:3 HYDROGENS=2-192:3,3-192:3 CLUSTERS=b3lyp.pamm 
+hbo: HBPAMM_SH SITES=1-192:3 HYDROGENS=2-192:3,3-192:3 CLUSTERS=b3lyp.pamm 
 
 DUMPMULTICOLVAR DATA=hbo PRECISION=4 FILE=hydrogens.xyz
 
-mata: HBPAMM ATOMS=52,58,175 CLUSTERS=b3lyp.pamm HYDROGENS=53,54,59,60,176,177 SUM 
-# matn: HBPAMM ATOMS=52,58,175 CLUSTERS=b3lyp.pamm HYDROGENS=53,54,59,60,176,177 SUM NUMERICAL_DERIVATIVES
+mata: HBPAMM_MATRIX ATOMS=52,58,175 CLUSTERS=b3lyp.pamm HYDROGENS=53,54,59,60,176,177 SUM 
+# matn: HBPAMM_MATRIX ATOMS=52,58,175 CLUSTERS=b3lyp.pamm HYDROGENS=53,54,59,60,176,177 SUM NUMERICAL_DERIVATIVES
 
 DUMPDERIVATIVES ARG=mata.* FILE=deriv FMT=%8.4f
 
-hpn: HBPAMM_PERH SITES=52,58,175 CLUSTERS=b3lyp.pamm HYDROGENS=53,54,59,60,176,177 SUM 
-# hpnn: HBPAMM_PERH SITES=52,58,175 CLUSTERS=b3lyp.pamm HYDROGENS=53,54,59,60,176,177 SUM NUMERICAL_DERIVATIVES
+hpn: HBPAMM_SH SITES=52,58,175 CLUSTERS=b3lyp.pamm HYDROGENS=53,54,59,60,176,177 SUM 
+# hpnn: HBPAMM_SH SITES=52,58,175 CLUSTERS=b3lyp.pamm HYDROGENS=53,54,59,60,176,177 SUM NUMERICAL_DERIVATIVES
 
 DUMPDERIVATIVES ARG=hpn.* FILE=deriv2 FMT=%8.4f