Added Bops Shortcut from Jake and regtests

regtest/crystdistrib/rt-bops-shortcut/Makefile

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

regtest/crystdistrib/rt-bops-shortcut/colvar.reference

@@ -0,0 +1,4 @@
+#! FIELDS time sdot.1 sdot.2 sdot.3 sdot.4 sdot.5 sdot.6 sdot.7 sdot.8 sdot.9 sdot.10 sdot.11 sdot.12 sdot.13 sdot.14 sdot.15 sdot.16 sdot.17 sdot.18 sdot.19 sdot.20 sdot.21 sdot.22 sdot.23 sdot.24 sdot.25 sdot.26 sdot.27 sdot.28 sdot.29 sdot.30 sdot.31 sdot.32 sdot.33 sdot.34 sdot.35 sdot.36 sdot.37 sdot.38 sdot.39 sdot.40 sdot.41 sdot.42 sdot.43 sdot.44 sdot.45 sdot.46 sdot.47 sdot.48 sdot.49 sdot.50 sdot.51 sdot.52 sdot.53 sdot.54 sdot.55 sdot.56 sdot.57 sdot.58 sdot.59 sdot.60 sdot.61 sdot.62 sdot.63 sdot.64 sdot.65 sdot.66 sdot.67 sdot.68 sdot.69 sdot.70 sdot.71 sdot.72 sdot.73 sdot.74 sdot.75 sdot.76 sdot.77 sdot.78 sdot.79 sdot.80 sdot.81 sdot.82 sdot.83 sdot.84 sdot.85 sdot.86 sdot.87 sdot.88 sdot.89 sdot.90 sdot.91 sdot.92 sdot.93 sdot.94 sdot.95 sdot.96 sdot.97 sdot.98 sdot.99 sdot.100 sdot.101 sdot.102 sdot.103 sdot.104 sdot.105 sdot.106 sdot.107 sdot.108 sdot.109 sdot.110 sdot.111 sdot.112 sdot.113 sdot.114 sdot.115 sdot.116 sdot.117 sdot.118 sdot.119 sdot.120 sdot.121 sdot.122 sdot.123 sdot.124 sdot.125 sdot.126 sdot.127 sdot.128 sdot.129 sdot.130 sdot.131 sdot.132 sdot.133 sdot.134 sdot.135 sdot.136 sdot.137 sdot.138 sdot.139 sdot.140 sdot.141 sdot.142 sdot.143 sdot.144 sdot.145 sdot.146 sdot.147 sdot.148 sdot.149 sdot.150 sdot.151 sdot.152 sdot.153 sdot.154 sdot.155 sdot.156 sdot.157 sdot.158 sdot.159 sdot.160 sdot.161 sdot.162 sdot.163 sdot.164 sdot.165 sdot.166 sdot.167 sdot.168 sdot.169 sdot.170 sdot.171 sdot.172 sdot.173 sdot.174 sdot.175 sdot.176 sdot.177 sdot.178 sdot.179 sdot.180 sdot.181 sdot.182 sdot.183 sdot.184 sdot.185 sdot.186 sdot.187 sdot.188 sdot.189 sdot.190 sdot.191 sdot.192 sdot.193 sdot.194 sdot.195 sdot.196 sdot.197 sdot.198 sdot.199 sdot.200 sdot.201 sdot.202 sdot.203 sdot.204 sdot.205 sdot.206 sdot.207 sdot.208 sdot.209 sdot.210 sdot.211 sdot.212 sdot.213 sdot.214 sdot.215 sdot.216 sdot.217 sdot.218 sdot.219 sdot.220 sdot.221 sdot.222 sdot.223 sdot.224 sdot.225 sdot.226 sdot.227 sdot.228 sdot.229 sdot.230 sdot.231 sdot.232 sdot.233 sdot.234 sdot.235 sdot.236 sdot.237 sdot.238 sdot.239 sdot.240 sdot.241 sdot.242 sdot.243 sdot.244 sdot.245 sdot.246 sdot.247 sdot.248 sdot.249 sdot.250 sdot.251 sdot.252
+ 0.000000   0.0000   0.0001   0.0000   1.3332   1.8329   2.3898   5.7497   1.6098   2.5381   0.6661   6.1629   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   1.7690   0.0388   0.0000   0.0000   0.0000   0.0000   0.0964   0.0040   4.4227   0.2300   0.2161   4.8042   1.8146   0.0000   0.4020   8.8096   0.7029   0.0077  11.9288   1.0983   0.0000   0.8314   0.0000   0.0000   0.0000   0.0000   0.0000   0.9004   0.0000   0.0275   4.7254   0.7013   1.4414   9.8804   0.5955   0.6058  21.3479   0.1959   0.8486   4.8835   0.0000   3.5685   3.5840   0.0000   0.8550   0.0240   0.0046   0.0000   1.1129   2.8897   3.3277   6.7606   4.5050   0.0555   5.4129   0.7391   0.0000   0.6294   0.0000   0.0000   0.0000   0.0014   0.0000   0.1115   1.9818   0.0000   0.1725   2.3816   0.0000   0.0001   5.6376   0.0000   0.0847   0.0002   0.0000  18.9813  10.2336   0.0000   4.1485   5.5364   0.4933   3.4929   0.0432   0.0000   0.0585   0.0000   0.0000   0.0069   0.0303   0.0000   1.9160   3.2395   0.0139   3.6720   4.1637   0.3699   4.1125   2.8084   0.0000   8.5729   2.3603   0.0000   5.9075   1.3916   0.0743   0.0001   0.0044   0.0000   0.0008   0.0266   6.2256   2.5003   0.7214   3.1874   7.9448   0.4617  13.2676   0.0000   0.0026   4.4009   0.0000   0.0237   0.0000   0.0000   0.1201   0.0000   0.0000   0.0002   0.0000   0.0034   0.0000   3.8442   1.5967   0.0001   3.2004   0.7253   0.0000   0.9909   6.8970   0.0000   5.0688   3.1785   0.0802   0.9688   1.2658   0.3720   0.0633   0.0000   0.0000   0.0001   0.0000   0.0000   0.0004   0.5549   0.0813   4.6613   1.2901   0.0025   2.0948   0.7776   0.5039   8.6393   1.2306   0.0868   1.8497   4.3774   0.0000   0.1296   0.0000   0.0000   0.0000   5.4154   0.0001   0.0000   0.0000   0.6360   1.9598   0.0000   0.0277   4.1845   0.0000   0.4054   1.0604   0.0001   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.3272   0.0000   0.0000   0.0756   0.0528   0.0000  14.1183   7.5987   0.0000   0.9613   0.9848   0.0000   9.9097   0.4329   0.0000  12.0364   0.5074   0.0000   1.2543   2.0302   0.0001   0.0000   0.1123   0.0784   0.0000   0.1351   0.0000   0.0521   0.0000   0.0198  16.7910  14.7826   0.0000  10.7352   3.0942   0.0524   4.6858  11.2648   0.0000   6.1599  10.8057   0.0000   1.2133   0.3753
+ 0.025000   0.0000   0.0002   0.0001   1.3992   2.0190   2.3168   7.0910   1.4305   2.6351   1.0584   7.4661   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   1.3304   0.0286   0.0000   0.0000   0.0000   0.0000   0.0389   0.0052   4.2083   0.2608   0.1722   4.3101   2.8648   0.0000   0.3616   7.4529   0.7378   0.0065  10.7460   1.4757   0.0000   0.5894   0.0000   0.0000   0.0000   0.0000   0.0000   1.7516   0.0000   0.0294   4.5327   0.8008   1.5832   8.7934   0.5348  10.7550  21.6150   0.1455   0.8597   5.5402   0.0000   4.1986   4.5348   0.0000   0.8009   0.0170   0.0108   0.0000   0.8951   2.8615   1.4921   7.3356   5.0563   0.1146   4.1951   1.2584   0.0000   2.8634   0.0000   0.0000   0.0000   0.0004   0.0000   0.1304   2.8264   0.0000   0.2520   2.3972   0.0000   0.0002   6.1518   0.0000   0.2854   0.0002   0.0000  15.4790   5.0386   0.0000   8.4074   6.8000   0.5361   3.5302   0.0672   0.0000   0.0434   0.0000   0.0000   0.0101   0.0190   0.0000   0.1585   3.9533   0.0341   3.7293   4.2397   3.2234   4.2874   3.0186   0.0000  19.2976   2.3655   0.0000   5.4496   1.3006   0.0894   0.0003   0.0069   0.0000   0.0005   0.0447   6.4206   9.1423   0.6533   4.8397  10.0559   0.4985  11.0001   0.0000   0.0015   9.2586   0.0000   0.0138   0.0000   0.0000   0.1056   0.0000   0.0000   0.0004   0.0000   0.0072   0.0000   4.5030   0.9736   0.0001   3.5804   2.3539   0.0000   1.6394   8.3161   0.0000   6.8648   2.4822   0.0830   4.5086   1.3035   0.4937   0.1718   0.0000   0.0000   0.0001   0.0000   0.0000   0.0002   0.5450   0.0729   0.8192   0.6566   0.0089   2.4356   0.7325   0.5273   6.0312   1.0655   0.0789   2.5132   5.5250   0.0000   0.1045   0.0000   0.0000   0.0000   6.8014   0.0002   0.0000   0.0000   0.5571   2.0174   0.0000   0.0510   4.9906   0.0000   0.2870   1.0876   0.0001   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.2973   0.0000   0.0000   0.0916   0.0674   0.0000  18.1283   5.9662   0.0000   2.6941   1.3144   0.0000  11.0358   0.6760   0.0000   7.8788   0.8554   0.0000   0.8368   1.8934   0.0000   0.0000   0.0094   0.0696   0.0000   0.1577   0.0000   0.0903   0.0000   0.0084   7.3972   5.8081   0.0000   9.7276   4.1920   0.0640  11.5746  11.7100   0.0000   1.3194   9.3225   0.0000   0.1829   0.2849
+ 0.050000   0.0000   0.0004   0.0004   1.8045   2.1892   2.3166   4.8580   1.4705   2.9920   1.8471   7.2616   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.6737   0.0011   0.0000   0.0000   0.0000   0.0000   4.0189   0.0146   4.9686   0.1586   0.1982   3.5325   1.6790   0.0000   0.4883   5.7627   0.5588   2.0330   8.9157   1.8044   0.0000   1.9977   0.0000   0.0000   0.0000   0.0000   0.0000   2.1859   0.0000   0.0346   3.1734   1.1682   1.7881   2.4270   0.6848   4.7905  21.0949   0.1564   0.8037  23.5400   1.4614   4.6885   4.0944   0.7288   1.0398   0.0252   0.0518   0.0000   0.2311   2.6632   2.5862  17.0818  15.2936   0.1536  14.5045  10.3211   0.0000   2.7641   0.0000   0.0000   0.0000   0.0001   0.0000   0.0493   0.0000   0.0000   2.8955   2.6449   0.0000   0.0006   7.0813   0.0000   0.7264   0.5336   0.0000  15.6594   4.2938   0.0000  13.5212   0.2846   0.2368   3.3855   0.6586   0.0000   0.0291   0.0000   0.0000   0.0153   0.0000   0.0000   0.0134   4.7655   0.0000   2.7407   6.9872   1.2314   3.7542   2.7240   0.0000  20.0844   1.5477   0.0000   6.8348   1.3206   0.0854   0.6125   0.0081   0.0000   0.0010   0.0557   4.3968  14.8277   0.9476   2.8385  12.7298   0.7703   1.0343   0.0000   0.0401  13.2741   0.0000   0.0000   0.0000   0.0000   0.0021   0.0000   0.0000   0.0023   0.0000   0.0343   0.0000   5.4020   0.6215   0.0000   2.9213   8.4090   0.0000   0.0000  11.7322   0.0000  13.7500   2.3873   0.0373  24.1800   1.3758   1.2135   0.9548   0.0000   0.0000   0.0004   0.0000   0.0000   0.0011   0.1306   0.0016   1.7570   1.8387   0.7617   3.1068   0.3695   0.6339   8.2020   0.9034   0.0932   2.8461   5.9198   0.0000   0.0633   0.0000   0.0000   0.0000   0.0000   0.0005   0.0000   0.0000   0.0796   2.2345   0.0000   0.1275   5.7372   0.0000   0.7428   1.0715   0.0002   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.1762   0.0000   0.0000   0.1115   0.1490   0.0000  18.7997   6.8848   0.0000   0.2046   2.3941   0.0000   9.1292   0.0000   0.0000  10.4722   1.1522   0.0000   0.6778   1.5178   0.0000   0.0000   0.0000   0.0329   2.9104   0.0812   0.0000   0.3248   0.0000   0.0000   3.2039  15.9435   0.0000   5.9970  14.4300   0.0473   3.2473   9.6505   0.0000   6.5803   5.2251   0.0000   0.4816   0.4053

regtest/crystdistrib/rt-bops-shortcut/config

@@ -0,0 +1,2 @@
+type=driver
+arg="--plumed plumed.dat --mf_xtc em.xtc --mc mcfile --timestep=0.001 --box 82.688,82.711,82.700 --trajectory-stride=25 --dump-forces forces --dump-forces-fmt=%8.4f"