Implemented a version of ActionVolume that works when the chains are …

…not used

regtest/symfunc/rt-q6-nochain/config

@@ -0,0 +1,13 @@
+type=driver
+plumed_modules=symfunc
+# this is to test a different name
+arg="--plumed plumed.dat --ixyz 64.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
+extra_files="../../trajectories/64.xyz"
+
+function plumed_regtest_before() {
+   export PLUMED_FORBID_CHAINS=yes
+} 
+
+function plumed_regtest_after() {
+   export PLUMED_FORBID_CHAINS=no
+}

regtest/symfunc/rt-q6-nochain/forces.reference

@@ -0,0 +1,66 @@
+64
+ -0.0519   0.1128   0.0399
+X  -0.0017  -0.0017  -0.0049
+X   0.0079  -0.0010   0.0191
+X  -0.0042  -0.0027   0.0191
+X   0.0045  -0.0010  -0.0068
+X   0.0001  -0.0001  -0.0001
+X   0.0004   0.0072   0.0002
+X   0.0069   0.0003   0.0000
+X   0.0015   0.0003   0.0023
+X  -0.0072   0.0040   0.0057
+X  -0.0023   0.0078  -0.0012
+X   0.0029  -0.0131  -0.0032
+X  -0.0033   0.0012  -0.0079
+X  -0.0002   0.0002   0.0054
+X  -0.0017  -0.0049  -0.0065
+X   0.0022  -0.0053  -0.0015
+X  -0.0113  -0.0021  -0.0040
+X   0.0040   0.0010   0.0038
+X   0.0027  -0.0047   0.0066
+X  -0.0000  -0.0066  -0.0076
+X   0.0008   0.0033   0.0064
+X   0.0007   0.0101   0.0022
+X   0.0087  -0.0100  -0.0074
+X   0.0004  -0.0031   0.0076
+X  -0.0045   0.0045   0.0019
+X  -0.0048  -0.0098  -0.0093
+X   0.0042   0.0076   0.0009
+X  -0.0060   0.0106   0.0006
+X   0.0031   0.0031  -0.0004
+X  -0.0034  -0.0012   0.0012
+X   0.0002   0.0075  -0.0214
+X  -0.0007  -0.0037  -0.0057
+X  -0.0081  -0.0026   0.0120
+X  -0.0061  -0.0051   0.0013
+X  -0.0005  -0.0022   0.0038
+X   0.0045   0.0058   0.0015
+X  -0.0149   0.0006  -0.0064
+X  -0.0011  -0.0127   0.0015
+X  -0.0012  -0.0023   0.0029
+X  -0.0085   0.0047   0.0120
+X  -0.0090  -0.0005  -0.0119
+X   0.0053   0.0054  -0.0036
+X  -0.0026   0.0051   0.0119
+X   0.0028   0.0041  -0.0008
+X  -0.0006   0.0136   0.0040
+X   0.0037  -0.0007   0.0078
+X  -0.0070   0.0022  -0.0096
+X  -0.0094   0.0005   0.0005
+X   0.0022  -0.0025  -0.0113
+X  -0.0033  -0.0013  -0.0012
+X   0.0076  -0.0015   0.0030
+X   0.0055  -0.0080  -0.0098
+X   0.0048  -0.0001   0.0062
+X  -0.0065   0.0024   0.0151
+X   0.0066   0.0061   0.0043
+X   0.0081   0.0085  -0.0119
+X  -0.0063   0.0047  -0.0134
+X  -0.0060  -0.0087  -0.0066
+X   0.0009  -0.0114  -0.0004
+X   0.0004   0.0097  -0.0144
+X   0.0117  -0.0026  -0.0020
+X   0.0007  -0.0015   0.0189
+X   0.0024   0.0105  -0.0025
+X   0.0088   0.0002  -0.0007
+X   0.0152  -0.0183   0.0046

regtest/symfunc/rt-q6-lowmem/plumed.dat → regtest/symfunc/rt-q6-nochain/plumed.dat

@@ -4,3 +4,4 @@ PRINT ARG=q6.* FILE=colv
 LOCAL_Q6 SPECIES=q6 SWITCH={RATIONAL D_0=3.0 R_0=1.5} MEAN LABEL=w6
 PRINT ARG=w6.* FILE=colv3
 
+BIASVALUE ARG=w6_mean

regtest/volumes/rt24/Makefile

@@ -0,0 +1 @@
+include ../../scripts/test.make

regtest/volumes/rt24/colvar.reference

@@ -0,0 +1,21 @@
+#! FIELDS time a1_lessthan a1_mean a2_lessthan a2_mean a3_lessthan a3_mean
+ 0.000000  24.6887   0.4844  29.5285   0.4089  26.2692   0.4855
+ 0.050000  21.4196   0.4812  24.2911   0.5046  20.4149   0.5235
+ 0.100000  24.0789   0.4990  19.5334   0.5008  17.5531   0.5338
+ 0.150000  24.7316   0.5294  20.8201   0.4740  18.3199   0.4995
+ 0.200000  20.5181   0.5141  20.7127   0.4958  24.2243   0.4777
+ 0.250000  14.5411   0.5384  24.0174   0.5035  23.1592   0.4681
+ 0.300000  20.7004   0.5109  18.6197   0.5132  21.1682   0.5299
+ 0.350000  13.9216   0.5851  22.7805   0.5168  17.5875   0.4531
+ 0.400000  23.2710   0.4804  18.4123   0.5179  21.2690   0.4777
+ 0.450000  14.0948   0.6024  25.6635   0.4871  19.0694   0.5803
+ 0.500000  18.3672   0.4938  21.0006   0.4583  21.0522   0.4942
+ 0.550000  16.7623   0.5342  23.0384   0.4970  17.5377   0.4665
+ 0.600000  15.8175   0.5281  16.6518   0.4914  16.6425   0.5568
+ 0.650000  20.4228   0.5089  17.4494   0.5079  24.4803   0.4642
+ 0.700000  24.7885   0.4666  15.1186   0.4913  24.6510   0.4331
+ 0.750000  30.4366   0.4697  25.4195   0.4175  27.7407   0.4897
+ 0.800000  25.1756   0.4427  23.2958   0.4730  27.8497   0.5077
+ 0.850000  22.8584   0.4854  19.4940   0.4654  18.5076   0.5486
+ 0.900000  14.8451   0.6134  20.0643   0.5444  18.1854   0.5895
+ 0.950000  20.2570   0.4676  23.0313   0.4860  23.2711   0.4263

regtest/volumes/rt24/config

@@ -0,0 +1,12 @@
+plumed_modules=volumes
+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
+
+function plumed_regtest_before() {
+   export PLUMED_FORBID_CHAINS=yes
+} 
+
+function plumed_regtest_after() {
+   export PLUMED_FORBID_CHAINS=no
+}

regtest/volumes/rt24/gentraj.cpp

@@ -0,0 +1,47 @@
+#include <stdlib.h>
+#include <math.h>
+#include <iostream>
+#include <vector>
+
+double randomn() { return rand()/static_cast<double>(RAND_MAX); }
+
+int main() {
+
+  std::vector<double> tot(8,0), dtot(8,0); bool dens=false;
+  unsigned nmols=200, dir; std::vector<double> com(3), dist(3), a1(3), a2(3), len(nmols);
+  for(unsigned i=0;i<20;++i){
+      if(dens) std::cout<<1+nmols<<std::endl;
+      else std::cout<<1+2*nmols<<std::endl;
+      std::cout<<10.0<<" "<<10.0<<" "<<10.0<<std::endl;
+      std::cout<<"Ar "<<5.0<<" "<<5.0<<" "<<5.0<<std::endl;
+      for(unsigned j=0;j<nmols;++j){
+         com[0]=10.0*randomn(); com[1]=10.0*randomn(); com[2]=10.0*randomn();
+         for(unsigned k=0;k<3;++k) dist[k]=fabs(com[k]-5.0);
+         len[j]=randomn(); dir=floor( 3*randomn() );
+         std::cout<<"LENGTH "<<len[j]<<std::endl;
+         if( dist[0]<1.0 ){ tot[1]+=1.0; dtot[1]+=len[j]; }
+         if( dist[1]<1.0 ){ tot[2]+=1.0; dtot[2]+=len[j]; }
+         if( dist[2]<1.0 ){ tot[3]+=1.0; dtot[3]+=len[j]; }
+         if( dist[0]<1.0 && dist[1]<1.0 ){ tot[4]+=1.0; dtot[4]+=len[j]; }
+         if( dist[0]<1.0 && dist[2]<1.0 ){ tot[5]+=1.0; dtot[5]+=len[j]; }
+         if( dist[1]<1.0 && dist[2]<1.0 ){ tot[6]+=1.0; dtot[6]+=len[j]; }
+         if( dist[0]<1.0 && dist[1]<1.0 && dist[2]<1.0 ){ tot[7]+=1.0; dtot[7]+=len[j]; }
+         a1[0]=com[0]; a1[1]=com[1]; a1[2]=com[2];
+         a2[0]=com[0]; a2[1]=com[1]; a2[2]=com[2];
+         a1[dir]-=0.5*len[j]; a2[dir]+=0.5*len[j];
+//         if(dens){
+//            std::cout<<"Ar "<<com[0]<<" "<<com[1]<<" "<<com[2]<<std::endl;
+//         } else {
+//            std::cout<<"Ar "<<a1[0]<<" "<<a1[1]<<" "<<a1[2]<<std::endl;
+//            std::cout<<"Ar "<<a2[0]<<" "<<a2[1]<<" "<<a2[2]<<std::endl;
+//         }
+      }
+      for(unsigned j=1;j<8;++j){
+         if(dens) std::cerr<<"CV "<<j<<" "<<tot[j]<<std::endl; 
+         else std::cerr<<"CV "<<j<<" "<<tot[j]<<" "<<dtot[j]<<" "<<dtot[j] / tot[j]<<std::endl;
+         tot[j]=dtot[j]=0.0;
+      }
+  }
+
+  return 1;
+}