diff --git a/regtest/ttsketch/rt-ttmetad-2/COLVAR.reference b/regtest/ttsketch/rt-ttmetad-2/COLVAR.reference new file mode 100644 index 0000000000..44a2f81dc0 --- /dev/null +++ b/regtest/ttsketch/rt-ttmetad-2/COLVAR.reference @@ -0,0 +1,24 @@ +#! FIELDS time phi psi tt.bias +#! SET min_phi -pi +#! SET max_phi pi + 0.000000 -1.2379 1.9470 5.0125 + 1.000000 -1.4839 1.9381 4.7386 + 2.000000 -1.3243 1.9663 5.7173 + 3.000000 -1.3340 1.9885 6.6124 + 4.000000 -1.4613 1.8901 6.9762 + 5.000000 -1.2202 2.0306 7.0226 + 6.000000 -1.3883 1.8776 8.4608 + 7.000000 -1.5481 1.9488 8.0675 + 8.000000 -1.8429 1.9025 4.8013 + 9.000000 -2.2424 1.9813 2.9942 + 10.000000 -1.1482 1.9684 7.7028 + 11.000000 -1.7580 1.9807 6.3092 + 12.000000 -1.3186 1.9486 7.0545 + 13.000000 -2.9911 1.9547 -0.0205 + 14.000000 -1.4112 2.0415 7.6081 + 15.000000 -2.5995 1.9166 2.0867 + 16.000000 -1.4608 1.9433 8.5441 + 17.000000 -1.3791 2.0625 8.9533 + 18.000000 -1.6771 1.9433 8.4947 + 19.000000 -1.5241 1.9642 10.3355 + 20.000000 -1.1997 1.9296 9.0332 diff --git a/regtest/ttsketch/rt-ttmetad-2/HILLS b/regtest/ttsketch/rt-ttmetad-2/HILLS new file mode 100644 index 0000000000..8841ba1482 --- /dev/null +++ b/regtest/ttsketch/rt-ttmetad-2/HILLS @@ -0,0 +1,4 @@ +#! FIELDS time phi psi sigma_phi sigma_psi height biasf +#! SET min_phi -pi +#! SET max_phi pi + 20.000000 -1.199652 1.929639 0.200000 0.200000 1.119533 10.000000 diff --git a/regtest/ttsketch/rt-ttmetad-2/HILLS.reference b/regtest/ttsketch/rt-ttmetad-2/HILLS.reference new file mode 100644 index 0000000000..7a38fbfc1e --- /dev/null +++ b/regtest/ttsketch/rt-ttmetad-2/HILLS.reference @@ -0,0 +1,4 @@ +#! FIELDS time phi psi sigma_phi sigma_psi height biasf +#! SET min_phi -pi +#! SET max_phi pi + 20.000000 -1.199652 1.929639 0.200000 0.200000 0.956750 10.000000 diff --git a/regtest/ttsketch/rt-ttmetad-2/Makefile b/regtest/ttsketch/rt-ttmetad-2/Makefile new file mode 100644 index 0000000000..3703b27cea --- /dev/null +++ b/regtest/ttsketch/rt-ttmetad-2/Makefile @@ -0,0 +1 @@ +include ../../scripts/test.make diff --git a/regtest/ttsketch/rt-ttmetad-2/config b/regtest/ttsketch/rt-ttmetad-2/config new file mode 100644 index 0000000000..6c0c53f78a --- /dev/null +++ b/regtest/ttsketch/rt-ttmetad-2/config @@ -0,0 +1,4 @@ +plumed_needs=libitensor +plumed_modules=ttsketch +type=driver +arg="--plumed plumed.dat --trajectory-stride 500 --timestep 0.002 --igro traj.gro --dump-forces forces --dump-forces-fmt %.4lf" diff --git a/regtest/ttsketch/rt-ttmetad-2/forces.reference b/regtest/ttsketch/rt-ttmetad-2/forces.reference new file mode 100644 index 0000000000..6de8227a4f --- /dev/null +++ b/regtest/ttsketch/rt-ttmetad-2/forces.reference @@ -0,0 +1,504 @@ +22 +0.3392 0.8024 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a/regtest/ttsketch/rt-ttmetad-2/plumed.dat b/regtest/ttsketch/rt-ttmetad-2/plumed.dat new file mode 100644 index 0000000000..1d02ca1479 --- /dev/null +++ b/regtest/ttsketch/rt-ttmetad-2/plumed.dat @@ -0,0 +1,24 @@ +phi: TORSION ATOMS=5,7,9,15 NOPBC +psi: ANGLE ATOMS=7,9,15 + +tt: TTMETAD ... + RESTART=YES + ARG=phi,psi + SIGMA=0.20,0.20 + HEIGHT=1.20 + PACE=500 + TEMP=300.0 + FILE=HILLS + FMT=%12.6f + BIASFACTOR=10 + SKETCH_RANK=2 + SKETCH_INITRANK=4 + SKETCH_PACE=5000 + INTERVAL_MIN=-3.14159,0.0 + INTERVAL_MAX=3.14159,3.14159 + SKETCH_NBASIS=5 + SKETCH_ALPHA=1.0 + DETERMINISTIC +... + +PRINT STRIDE=500 FILE=COLVAR ARG=phi,psi,tt.bias FMT=%8.4f diff --git a/regtest/ttsketch/rt-ttmetad-2/traj.gro b/regtest/ttsketch/rt-ttmetad-2/traj.gro new file mode 100644 index 0000000000..c1c387a014 --- /dev/null +++ b/regtest/ttsketch/rt-ttmetad-2/traj.gro @@ -0,0 +1,525 @@ +Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 0.00000 + 22 + 1ACE HH31 1 1.474 1.585 1.200 + 1ACE CH3 2 1.483 1.508 1.277 + 1ACE HH32 3 1.476 1.561 1.372 + 1ACE HH33 4 1.578 1.455 1.278 + 1ACE C 5 1.353 1.428 1.279 + 1ACE O 6 1.263 1.449 1.357 + 2ALA N 7 1.343 1.328 1.191 + 2ALA H 8 1.415 1.321 1.120 + 2ALA CA 9 1.233 1.239 1.159 + 2ALA HA 10 1.144 1.302 1.155 + 2ALA CB 11 1.244 1.182 1.013 + 2ALA HB1 12 1.341 1.136 0.992 + 2ALA HB2 13 1.159 1.117 0.994 + 2ALA HB3 14 1.242 1.265 0.942 + 2ALA C 15 1.207 1.140 1.271 + 2ALA O 16 1.214 1.017 1.241 + 3NME N 17 1.191 1.177 1.398 + 3NME H 18 1.192 1.275 1.421 + 3NME CH3 19 1.189 1.086 1.518 + 3NME HH31 20 1.170 0.983 1.487 + 3NME HH32 21 1.283 1.087 1.574 + 3NME HH33 22 1.108 1.127 1.578 + 10.00000 10.00000 10.00000 +Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 1.00000 + 22 + 1ACE HH31 1 1.480 1.571 1.214 + 1ACE CH3 2 1.481 1.493 1.289 + 1ACE HH32 3 1.502 1.528 1.390 + 1ACE HH33 4 1.551 1.417 1.255 + 1ACE C 5 1.344 1.432 1.275 + 1ACE O 6 1.250 1.462 1.345 + 2ALA N 7 1.342 1.327 1.193 + 2ALA H 8 1.430 1.313 1.144 + 2ALA CA 9 1.233 1.244 1.166 + 2ALA HA 10 1.144 1.307 1.173 + 2ALA CB 11 1.240 1.189 1.017 + 2ALA HB1 12 1.327 1.124 1.000 + 2ALA HB2 13 1.150 1.128 1.005 + 2ALA HB3 14 1.251 1.267 0.941 + 2ALA C 15 1.221 1.133 1.271 + 2ALA O 16 1.217 1.015 1.238 + 3NME N 17 1.204 1.174 1.395 + 3NME H 18 1.200 1.275 1.398 + 3NME CH3 19 1.188 1.089 1.516 + 3NME HH31 20 1.083 1.086 1.543 + 3NME HH32 21 1.233 0.990 1.511 + 3NME HH33 22 1.241 1.141 1.596 + 10.00000 10.00000 10.00000 +Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 2.00000 + 22 + 1ACE HH31 1 1.532 1.520 1.209 + 1ACE CH3 2 1.478 1.493 1.300 + 1ACE HH32 3 1.465 1.586 1.356 + 1ACE HH33 4 1.548 1.426 1.350 + 1ACE C 5 1.352 1.423 1.279 + 1ACE O 6 1.252 1.461 1.340 + 2ALA N 7 1.351 1.326 1.190 + 2ALA H 8 1.442 1.293 1.160 + 2ALA CA 9 1.232 1.244 1.160 + 2ALA HA 10 1.146 1.310 1.151 + 2ALA CB 11 1.241 1.190 1.016 + 2ALA HB1 12 1.333 1.132 1.008 + 2ALA HB2 13 1.160 1.123 0.986 + 2ALA HB3 14 1.242 1.280 0.955 + 2ALA C 15 1.203 1.138 1.270 + 2ALA O 16 1.161 1.021 1.240 + 3NME N 17 1.230 1.171 1.396 + 3NME H 18 1.257 1.266 1.417 + 3NME CH3 19 1.217 1.090 1.512 + 3NME HH31 20 1.144 1.011 1.493 + 3NME HH32 21 1.307 1.029 1.526 + 3NME HH33 22 1.212 1.146 1.605 + 10.00000 10.00000 10.00000 +Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 3.00000 + 22 + 1ACE HH31 1 1.439 1.582 1.175 + 1ACE CH3 2 1.474 1.516 1.254 + 1ACE HH32 3 1.480 1.585 1.338 + 1ACE HH33 4 1.569 1.465 1.242 + 1ACE C 5 1.364 1.419 1.280 + 1ACE O 6 1.277 1.446 1.367 + 2ALA N 7 1.358 1.323 1.194 + 2ALA H 8 1.443 1.313 1.140 + 2ALA CA 9 1.235 1.243 1.164 + 2ALA HA 10 1.150 1.310 1.170 + 2ALA CB 11 1.240 1.197 1.019 + 2ALA HB1 12 1.316 1.119 1.016 + 2ALA HB2 13 1.145 1.157 0.982 + 2ALA HB3 14 1.279 1.276 0.955 + 2ALA C 15 1.201 1.137 1.272 + 2ALA O 16 1.172 1.021 1.232 + 3NME N 17 1.218 1.166 1.402 + 3NME H 18 1.240 1.259 1.434 + 3NME CH3 19 1.186 1.086 1.518 + 3NME HH31 20 1.225 0.984 1.527 + 3NME HH32 21 1.193 1.134 1.616 + 3NME HH33 22 1.081 1.058 1.509 + 10.00000 10.00000 10.00000 +Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 4.00000 + 22 + 1ACE HH31 1 1.549 1.508 1.196 + 1ACE CH3 2 1.500 1.486 1.290 + 1ACE HH32 3 1.487 1.571 1.357 + 1ACE HH33 4 1.563 1.415 1.343 + 1ACE C 5 1.362 1.425 1.270 + 1ACE O 6 1.265 1.465 1.340 + 2ALA N 7 1.349 1.324 1.182 + 2ALA H 8 1.432 1.287 1.138 + 2ALA CA 9 1.221 1.249 1.168 + 2ALA HA 10 1.138 1.318 1.184 + 2ALA CB 11 1.201 1.194 1.025 + 2ALA HB1 12 1.276 1.117 1.005 + 2ALA HB2 13 1.096 1.165 1.014 + 2ALA HB3 14 1.229 1.265 0.947 + 2ALA C 15 1.217 1.141 1.275 + 2ALA O 16 1.234 1.024 1.243 + 3NME N 17 1.183 1.174 1.400 + 3NME H 18 1.184 1.274 1.412 + 3NME CH3 19 1.187 1.078 1.509 + 3NME HH31 20 1.248 0.990 1.490 + 3NME HH32 21 1.220 1.120 1.604 + 3NME HH33 22 1.088 1.035 1.527 + 10.00000 10.00000 10.00000 +Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 5.00000 + 22 + 1ACE HH31 1 1.449 1.585 1.168 + 1ACE CH3 2 1.479 1.518 1.248 + 1ACE HH32 3 1.523 1.577 1.328 + 1ACE HH33 4 1.565 1.461 1.213 + 1ACE C 5 1.364 1.422 1.284 + 1ACE O 6 1.305 1.438 1.389 + 2ALA N 7 1.347 1.326 1.187 + 2ALA H 8 1.423 1.328 1.122 + 2ALA CA 9 1.226 1.241 1.162 + 2ALA HA 10 1.139 1.308 1.162 + 2ALA CB 11 1.236 1.193 1.023 + 2ALA HB1 12 1.314 1.117 1.012 + 2ALA HB2 13 1.137 1.167 0.986 + 2ALA HB3 14 1.273 1.278 0.966 + 2ALA C 15 1.195 1.133 1.268 + 2ALA O 16 1.173 1.016 1.239 + 3NME N 17 1.204 1.175 1.393 + 3NME H 18 1.211 1.275 1.403 + 3NME CH3 19 1.188 1.090 1.513 + 3NME HH31 20 1.089 1.044 1.509 + 3NME HH32 21 1.267 1.014 1.509 + 3NME HH33 22 1.189 1.145 1.607 + 10.00000 10.00000 10.00000 +Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 6.00000 + 22 + 1ACE HH31 1 1.517 1.511 1.181 + 1ACE CH3 2 1.490 1.488 1.284 + 1ACE HH32 3 1.482 1.582 1.339 + 1ACE HH33 4 1.569 1.421 1.316 + 1ACE C 5 1.359 1.414 1.282 + 1ACE O 6 1.272 1.447 1.358 + 2ALA N 7 1.351 1.320 1.186 + 2ALA H 8 1.434 1.297 1.133 + 2ALA CA 9 1.220 1.251 1.159 + 2ALA HA 10 1.139 1.323 1.167 + 2ALA CB 11 1.220 1.194 1.018 + 2ALA HB1 12 1.298 1.120 1.003 + 2ALA HB2 13 1.120 1.158 0.994 + 2ALA HB3 14 1.224 1.286 0.960 + 2ALA C 15 1.201 1.139 1.270 + 2ALA O 16 1.190 1.022 1.239 + 3NME N 17 1.203 1.178 1.393 + 3NME H 18 1.207 1.277 1.409 + 3NME CH3 19 1.211 1.102 1.515 + 3NME HH31 20 1.111 1.064 1.534 + 3NME HH32 21 1.275 1.017 1.492 + 3NME HH33 22 1.264 1.151 1.597 + 10.00000 10.00000 10.00000 +Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 7.00000 + 22 + 1ACE HH31 1 1.483 1.590 1.185 + 1ACE CH3 2 1.505 1.501 1.245 + 1ACE HH32 3 1.538 1.533 1.344 + 1ACE HH33 4 1.580 1.430 1.209 + 1ACE C 5 1.379 1.418 1.267 + 1ACE O 6 1.298 1.443 1.349 + 2ALA N 7 1.360 1.320 1.187 + 2ALA H 8 1.426 1.297 1.114 + 2ALA CA 9 1.224 1.253 1.180 + 2ALA HA 10 1.147 1.326 1.205 + 2ALA CB 11 1.174 1.215 1.037 + 2ALA HB1 12 1.245 1.152 0.983 + 2ALA HB2 13 1.084 1.154 1.032 + 2ALA HB3 14 1.153 1.311 0.992 + 2ALA C 15 1.212 1.141 1.280 + 2ALA O 16 1.219 1.022 1.244 + 3NME N 17 1.191 1.176 1.408 + 3NME H 18 1.207 1.275 1.423 + 3NME CH3 19 1.162 1.068 1.509 + 3NME HH31 20 1.229 0.982 1.503 + 3NME HH32 21 1.162 1.109 1.610 + 3NME HH33 22 1.056 1.044 1.499 + 10.00000 10.00000 10.00000 +Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 8.00000 + 22 + 1ACE HH31 1 1.576 1.425 1.169 + 1ACE CH3 2 1.523 1.455 1.260 + 1ACE HH32 3 1.547 1.556 1.294 + 1ACE HH33 4 1.566 1.393 1.338 + 1ACE C 5 1.385 1.422 1.255 + 1ACE O 6 1.308 1.499 1.305 + 2ALA N 7 1.346 1.311 1.189 + 2ALA H 8 1.419 1.248 1.159 + 2ALA CA 9 1.210 1.260 1.193 + 2ALA HA 10 1.139 1.326 1.242 + 2ALA CB 11 1.152 1.252 1.051 + 2ALA HB1 12 1.230 1.210 0.987 + 2ALA HB2 13 1.066 1.185 1.052 + 2ALA HB3 14 1.127 1.354 1.024 + 2ALA C 15 1.206 1.136 1.282 + 2ALA O 16 1.195 1.023 1.229 + 3NME N 17 1.210 1.152 1.420 + 3NME H 18 1.221 1.243 1.463 + 3NME CH3 19 1.185 1.048 1.518 + 3NME HH31 20 1.195 0.948 1.475 + 3NME HH32 21 1.261 1.070 1.593 + 3NME HH33 22 1.088 1.064 1.565 + 10.00000 10.00000 10.00000 +Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 9.00000 + 22 + 1ACE HH31 1 1.515 1.474 1.040 + 1ACE CH3 2 1.535 1.461 1.147 + 1ACE HH32 3 1.561 1.560 1.184 + 1ACE HH33 4 1.612 1.386 1.165 + 1ACE C 5 1.406 1.430 1.217 + 1ACE O 6 1.361 1.502 1.307 + 2ALA N 7 1.345 1.316 1.190 + 2ALA H 8 1.384 1.254 1.121 + 2ALA CA 9 1.217 1.277 1.242 + 2ALA HA 10 1.187 1.348 1.319 + 2ALA CB 11 1.111 1.278 1.134 + 2ALA HB1 12 1.129 1.198 1.062 + 2ALA HB2 13 1.018 1.269 1.189 + 2ALA HB3 14 1.121 1.372 1.079 + 2ALA C 15 1.217 1.133 1.309 + 2ALA O 16 1.293 1.044 1.265 + 3NME N 17 1.132 1.116 1.408 + 3NME H 18 1.076 1.195 1.437 + 3NME CH3 19 1.112 1.003 1.490 + 3NME HH31 20 1.156 0.910 1.456 + 3NME HH32 21 1.153 1.026 1.588 + 3NME HH33 22 1.005 0.985 1.500 + 10.00000 10.00000 10.00000 +Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 10.00000 + 22 + 1ACE HH31 1 1.536 1.485 1.135 + 1ACE CH3 2 1.521 1.460 1.240 + 1ACE HH32 3 1.528 1.557 1.289 + 1ACE HH33 4 1.602 1.397 1.276 + 1ACE C 5 1.385 1.401 1.261 + 1ACE O 6 1.341 1.416 1.373 + 2ALA N 7 1.322 1.332 1.167 + 2ALA H 8 1.364 1.316 1.076 + 2ALA CA 9 1.190 1.273 1.177 + 2ALA HA 10 1.125 1.352 1.216 + 2ALA CB 11 1.134 1.230 1.038 + 2ALA HB1 12 1.167 1.128 1.016 + 2ALA HB2 13 1.026 1.238 1.046 + 2ALA HB3 14 1.174 1.287 0.953 + 2ALA C 15 1.183 1.157 1.283 + 2ALA O 16 1.111 1.061 1.259 + 3NME N 17 1.264 1.157 1.396 + 3NME H 18 1.320 1.241 1.405 + 3NME CH3 19 1.264 1.070 1.510 + 3NME HH31 20 1.163 1.057 1.548 + 3NME HH32 21 1.311 0.974 1.487 + 3NME HH33 22 1.326 1.109 1.592 + 10.00000 10.00000 10.00000 +Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 11.00000 + 22 + 1ACE HH31 1 1.607 1.359 1.178 + 1ACE CH3 2 1.535 1.442 1.176 + 1ACE HH32 3 1.521 1.470 1.072 + 1ACE HH33 4 1.569 1.533 1.224 + 1ACE C 5 1.402 1.412 1.242 + 1ACE O 6 1.368 1.454 1.350 + 2ALA N 7 1.319 1.332 1.177 + 2ALA H 8 1.363 1.279 1.103 + 2ALA CA 9 1.194 1.289 1.231 + 2ALA HA 10 1.153 1.355 1.308 + 2ALA CB 11 1.092 1.300 1.113 + 2ALA HB1 12 1.137 1.243 1.032 + 2ALA HB2 13 1.001 1.243 1.131 + 2ALA HB3 14 1.070 1.405 1.095 + 2ALA C 15 1.198 1.143 1.290 + 2ALA O 16 1.237 1.057 1.213 + 3NME N 17 1.171 1.126 1.422 + 3NME H 18 1.164 1.213 1.472 + 3NME CH3 19 1.200 1.009 1.496 + 3NME HH31 20 1.118 0.938 1.493 + 3NME HH32 21 1.284 0.953 1.454 + 3NME HH33 22 1.230 1.031 1.598 + 10.00000 10.00000 10.00000 +Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 12.00000 + 22 + 1ACE HH31 1 1.491 1.569 1.138 + 1ACE CH3 2 1.511 1.462 1.134 + 1ACE HH32 3 1.614 1.449 1.166 + 1ACE HH33 4 1.495 1.444 1.028 + 1ACE C 5 1.416 1.394 1.229 + 1ACE O 6 1.445 1.392 1.345 + 2ALA N 7 1.299 1.357 1.181 + 2ALA H 8 1.278 1.358 1.082 + 2ALA CA 9 1.196 1.301 1.267 + 2ALA HA 10 1.185 1.364 1.355 + 2ALA CB 11 1.063 1.319 1.182 + 2ALA HB1 12 1.057 1.248 1.100 + 2ALA HB2 13 0.976 1.288 1.240 + 2ALA HB3 14 1.037 1.423 1.161 + 2ALA C 15 1.226 1.161 1.304 + 2ALA O 16 1.317 1.094 1.258 + 3NME N 17 1.135 1.110 1.387 + 3NME H 18 1.064 1.174 1.419 + 3NME CH3 19 1.121 0.972 1.429 + 3NME HH31 20 1.163 0.900 1.358 + 3NME HH32 21 1.177 0.954 1.520 + 3NME HH33 22 1.016 0.942 1.428 + 10.00000 10.00000 10.00000 +Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 13.00000 + 22 + 1ACE HH31 1 1.528 1.537 1.077 + 1ACE CH3 2 1.543 1.448 1.137 + 1ACE HH32 3 1.634 1.463 1.195 + 1ACE HH33 4 1.560 1.362 1.072 + 1ACE C 5 1.421 1.428 1.229 + 1ACE O 6 1.396 1.520 1.301 + 2ALA N 7 1.355 1.314 1.219 + 2ALA H 8 1.385 1.241 1.156 + 2ALA CA 9 1.249 1.276 1.311 + 2ALA HA 10 1.297 1.288 1.409 + 2ALA CB 11 1.122 1.359 1.284 + 2ALA HB1 12 1.072 1.325 1.193 + 2ALA HB2 13 1.053 1.352 1.367 + 2ALA HB3 14 1.153 1.463 1.275 + 2ALA C 15 1.204 1.131 1.290 + 2ALA O 16 1.225 1.070 1.185 + 3NME N 17 1.131 1.077 1.382 + 3NME H 18 1.104 1.132 1.463 + 3NME CH3 19 1.083 0.939 1.380 + 3NME HH31 20 1.012 0.925 1.298 + 3NME HH32 21 1.168 0.871 1.372 + 3NME HH33 22 1.036 0.915 1.475 + 10.00000 10.00000 10.00000 +Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 14.00000 + 22 + 1ACE HH31 1 1.543 1.468 1.123 + 1ACE CH3 2 1.548 1.443 1.229 + 1ACE HH32 3 1.566 1.540 1.276 + 1ACE HH33 4 1.634 1.382 1.257 + 1ACE C 5 1.420 1.385 1.285 + 1ACE O 6 1.412 1.375 1.404 + 2ALA N 7 1.324 1.361 1.200 + 2ALA H 8 1.345 1.354 1.101 + 2ALA CA 9 1.189 1.323 1.244 + 2ALA HA 10 1.163 1.394 1.323 + 2ALA CB 11 1.094 1.344 1.125 + 2ALA HB1 12 1.098 1.270 1.045 + 2ALA HB2 13 0.995 1.352 1.170 + 2ALA HB3 14 1.120 1.440 1.079 + 2ALA C 15 1.166 1.169 1.284 + 2ALA O 16 1.055 1.145 1.330 + 3NME N 17 1.263 1.077 1.279 + 3NME H 18 1.356 1.102 1.247 + 3NME CH3 19 1.246 0.942 1.335 + 3NME HH31 20 1.142 0.911 1.345 + 3NME HH32 21 1.293 0.868 1.270 + 3NME HH33 22 1.292 0.934 1.434 + 10.00000 10.00000 10.00000 +Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 15.00000 + 22 + 1ACE HH31 1 1.508 1.417 1.043 + 1ACE CH3 2 1.539 1.448 1.143 + 1ACE HH32 3 1.565 1.553 1.146 + 1ACE HH33 4 1.630 1.395 1.169 + 1ACE C 5 1.438 1.410 1.253 + 1ACE O 6 1.429 1.471 1.356 + 2ALA N 7 1.348 1.327 1.217 + 2ALA H 8 1.362 1.285 1.126 + 2ALA CA 9 1.233 1.289 1.298 + 2ALA HA 10 1.269 1.295 1.401 + 2ALA CB 11 1.107 1.379 1.286 + 2ALA HB1 12 1.057 1.360 1.191 + 2ALA HB2 13 1.034 1.369 1.366 + 2ALA HB3 14 1.141 1.482 1.282 + 2ALA C 15 1.192 1.141 1.266 + 2ALA O 16 1.220 1.089 1.156 + 3NME N 17 1.131 1.075 1.364 + 3NME H 18 1.117 1.126 1.450 + 3NME CH3 19 1.090 0.931 1.376 + 3NME HH31 20 1.156 0.880 1.446 + 3NME HH32 21 0.996 0.929 1.431 + 3NME HH33 22 1.090 0.874 1.283 + 10.00000 10.00000 10.00000 +Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 16.00000 + 22 + 1ACE HH31 1 1.587 1.386 1.166 + 1ACE CH3 2 1.554 1.425 1.262 + 1ACE HH32 3 1.559 1.534 1.266 + 1ACE HH33 4 1.627 1.390 1.335 + 1ACE C 5 1.417 1.372 1.300 + 1ACE O 6 1.390 1.364 1.421 + 2ALA N 7 1.334 1.344 1.205 + 2ALA H 8 1.365 1.367 1.111 + 2ALA CA 9 1.190 1.324 1.235 + 2ALA HA 10 1.160 1.386 1.319 + 2ALA CB 11 1.105 1.363 1.112 + 2ALA HB1 12 1.129 1.297 1.029 + 2ALA HB2 13 0.999 1.351 1.131 + 2ALA HB3 14 1.125 1.467 1.088 + 2ALA C 15 1.162 1.180 1.282 + 2ALA O 16 1.054 1.128 1.258 + 3NME N 17 1.261 1.106 1.318 + 3NME H 18 1.349 1.152 1.336 + 3NME CH3 19 1.250 0.960 1.324 + 3NME HH31 20 1.264 0.908 1.229 + 3NME HH32 21 1.322 0.926 1.399 + 3NME HH33 22 1.153 0.923 1.357 + 10.00000 10.00000 10.00000 +Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 17.00000 + 22 + 1ACE HH31 1 1.614 1.382 1.173 + 1ACE CH3 2 1.559 1.432 1.253 + 1ACE HH32 3 1.547 1.532 1.213 + 1ACE HH33 4 1.625 1.444 1.339 + 1ACE C 5 1.426 1.380 1.288 + 1ACE O 6 1.411 1.348 1.406 + 2ALA N 7 1.325 1.370 1.200 + 2ALA H 8 1.341 1.388 1.102 + 2ALA CA 9 1.189 1.318 1.239 + 2ALA HA 10 1.170 1.358 1.338 + 2ALA CB 11 1.084 1.388 1.158 + 2ALA HB1 12 1.113 1.369 1.055 + 2ALA HB2 13 0.994 1.336 1.189 + 2ALA HB3 14 1.075 1.493 1.186 + 2ALA C 15 1.170 1.163 1.252 + 2ALA O 16 1.097 1.103 1.171 + 3NME N 17 1.235 1.099 1.349 + 3NME H 18 1.305 1.153 1.399 + 3NME CH3 19 1.220 0.964 1.393 + 3NME HH31 20 1.315 0.912 1.406 + 3NME HH32 21 1.168 0.953 1.489 + 3NME HH33 22 1.178 0.897 1.318 + 10.00000 10.00000 10.00000 +Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 18.00000 + 22 + 1ACE HH31 1 1.555 1.419 1.126 + 1ACE CH3 2 1.554 1.431 1.235 + 1ACE HH32 3 1.554 1.535 1.267 + 1ACE HH33 4 1.638 1.381 1.283 + 1ACE C 5 1.423 1.378 1.292 + 1ACE O 6 1.416 1.347 1.409 + 2ALA N 7 1.322 1.351 1.211 + 2ALA H 8 1.350 1.370 1.115 + 2ALA CA 9 1.185 1.318 1.251 + 2ALA HA 10 1.171 1.358 1.352 + 2ALA CB 11 1.091 1.400 1.149 + 2ALA HB1 12 1.059 1.346 1.060 + 2ALA HB2 13 1.008 1.443 1.205 + 2ALA HB3 14 1.154 1.480 1.109 + 2ALA C 15 1.163 1.166 1.255 + 2ALA O 16 1.060 1.108 1.214 + 3NME N 17 1.255 1.102 1.328 + 3NME H 18 1.335 1.159 1.354 + 3NME CH3 19 1.246 0.964 1.369 + 3NME HH31 20 1.154 0.913 1.344 + 3NME HH32 21 1.323 0.899 1.327 + 3NME HH33 22 1.251 0.953 1.477 + 10.00000 10.00000 10.00000 +Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 19.00000 + 22 + 1ACE HH31 1 1.559 1.326 1.133 + 1ACE CH3 2 1.552 1.413 1.200 + 1ACE HH32 3 1.538 1.504 1.142 + 1ACE HH33 4 1.631 1.428 1.273 + 1ACE C 5 1.426 1.375 1.280 + 1ACE O 6 1.428 1.345 1.398 + 2ALA N 7 1.319 1.363 1.209 + 2ALA H 8 1.322 1.382 1.110 + 2ALA CA 9 1.191 1.329 1.265 + 2ALA HA 10 1.186 1.364 1.368 + 2ALA CB 11 1.075 1.391 1.178 + 2ALA HB1 12 1.098 1.383 1.072 + 2ALA HB2 13 0.980 1.348 1.211 + 2ALA HB3 14 1.066 1.499 1.192 + 2ALA C 15 1.169 1.174 1.275 + 2ALA O 16 1.086 1.118 1.203 + 3NME N 17 1.233 1.105 1.363 + 3NME H 18 1.312 1.150 1.405 + 3NME CH3 19 1.242 0.956 1.350 + 3NME HH31 20 1.219 0.899 1.440 + 3NME HH32 21 1.165 0.918 1.284 + 3NME HH33 22 1.333 0.921 1.301 + 10.00000 10.00000 10.00000 +Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 20.00000 + 22 + 1ACE HH31 1 1.622 1.459 1.287 + 1ACE CH3 2 1.546 1.434 1.214 + 1ACE HH32 3 1.578 1.365 1.135 + 1ACE HH33 4 1.509 1.531 1.180 + 1ACE C 5 1.430 1.358 1.283 + 1ACE O 6 1.444 1.310 1.394 + 2ALA N 7 1.315 1.370 1.215 + 2ALA H 8 1.323 1.427 1.132 + 2ALA CA 9 1.178 1.334 1.258 + 2ALA HA 10 1.163 1.376 1.357 + 2ALA CB 11 1.079 1.393 1.158 + 2ALA HB1 12 1.096 1.348 1.060 + 2ALA HB2 13 0.979 1.367 1.192 + 2ALA HB3 14 1.087 1.501 1.165 + 2ALA C 15 1.163 1.177 1.270 + 2ALA O 16 1.073 1.114 1.216 + 3NME N 17 1.249 1.110 1.347 + 3NME H 18 1.324 1.165 1.388 + 3NME CH3 19 1.242 0.964 1.360 + 3NME HH31 20 1.325 0.920 1.416 + 3NME HH32 21 1.151 0.938 1.414 + 3NME HH33 22 1.221 0.913 1.266 + 10.00000 10.00000 10.00000 diff --git a/regtest/ttsketch/rt-ttmetad-2/ttsketch.h5 b/regtest/ttsketch/rt-ttmetad-2/ttsketch.h5 new file mode 100644 index 0000000000..bc600f9723 Binary files /dev/null and b/regtest/ttsketch/rt-ttmetad-2/ttsketch.h5 differ diff --git a/src/ttsketch/TTHelper.cpp b/src/ttsketch/TTHelper.cpp index 8d51193ea5..1730c46016 100644 --- a/src/ttsketch/TTHelper.cpp +++ b/src/ttsketch/TTHelper.cpp @@ -4,6 +4,7 @@ See the COPYRIGHT file distributed with this software for license details. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ #include "TTHelper.h" +#include "tools/OpenMP.h" #ifdef __PLUMED_HAS_LIBITENSOR #ifdef __PLUMED_HAS_LIBHDF5 @@ -20,8 +21,7 @@ void ttWrite(const std::string& filename, const MPS& tt, unsigned count) { MPS ttRead(const std::string& filename, unsigned count) { auto f = h5_open(filename, 'r'); - auto tt = h5_read(f, "tt_" + std::to_string(count - 1)); - return tt; + return h5_read(f, "tt_" + std::to_string(count - 1)); } void ttSumWrite(const std::string& filename, const MPS& tt, unsigned count) { @@ -31,54 +31,69 @@ void ttSumWrite(const std::string& filename, const MPS& tt, unsigned count) { MPS ttSumRead(const std::string& filename, unsigned count) { auto f = h5_open(filename, 'r'); - auto tt = h5_read(f, "vb_" + std::to_string(count - 1)); - return tt; + return h5_read(f, "vb_" + std::to_string(count - 1)); } -// Evaluate TT by contracting each core with its 1D basis vector phi(x_i): -// result = sum_{i_1,...,i_d} G_1[i_1] * ... * G_d[i_d] * phi_1(x_1,i_1) * ... * phi_d(x_d,i_d) -// The contraction is performed left-to-right so intermediate results stay rank-1 scalars. -double ttEval(const MPS& tt, const std::vector& basis, const std::vector& elements, bool conv) { +// Evaluate TT and gradient together using a prefix-suffix sweep: O(d) contractions. +// +// For a TT of length d: +// L[i] = (G_1 * phi_1) * ... * (G_i * phi_i) [left partial product up to i] +// R[i] = (G_i * phi_i) * ... * (G_d * phi_d) [right partial product from i] +// +// val = elt(L[d]) +// grad[k] = L[k-1] * (G_k * dphi_k) * R[k+1] +std::pair> + ttEvalAndGrad(const itensor::MPS& tt, + const std::vector& basis, + const std::vector& elements, +bool conv) { int d = length(tt); auto s = siteInds(tt); - std::vector basis_evals(d); - for(int i = 1; i <= d; ++i) { - basis_evals[i - 1] = ITensor(s(i)); - for(int j = 1; j <= dim(s(i)); ++j) { - basis_evals[i - 1].set(s(i) = j, basis[i - 1](elements[i - 1], j, conv)); + const unsigned nt = OpenMP::getNumThreads(); + + // Cache cores and build phi/dphi — all independent across dimensions + std::vector cores(d), phi(d), dphi(d); + #pragma omp parallel for num_threads(nt) schedule(static) + for (int i = 0; i < d; ++i) { + cores[i] = tt(i + 1); + phi[i] = dphi[i] = ITensor(s(i + 1)); + for (int j = 1; j <= dim(s(i + 1)); ++j) { + phi[i].set(s(i + 1) = j, basis[i](elements[i], j, conv)); + dphi[i].set(s(i + 1) = j, basis[i].grad(elements[i], j, conv)); } } - auto result = tt(1) * basis_evals[0]; - for(int i = 2; i <= d; ++i) { - result *= tt(i) * basis_evals[i - 1]; - } - return elt(result); -} -// Gradient of ttEval w.r.t. elements. For each dimension k, one TT contraction is performed -// with the k-th basis vector replaced by its derivative d phi_k/dx_k (chain rule). -// All basis evaluations are precomputed to avoid redundant work across the d contractions. -std::vector ttGrad(const MPS& tt, const std::vector& basis, const std::vector& elements, bool conv) { - int d = length(tt); - auto s = siteInds(tt); - std::vector grad(d, 0.0); - std::vector basis_evals(d), basisd_evals(d); - for(int i = 1; i <= d; ++i) { - basis_evals[i - 1] = basisd_evals[i - 1] = ITensor(s(i)); - for(int j = 1; j <= dim(s(i)); ++j) { - basis_evals[i - 1].set(s(i) = j, basis[i - 1](elements[i - 1], j, conv)); - basisd_evals[i - 1].set(s(i) = j, basis[i - 1].grad(elements[i - 1], j, conv)); - } + // Prefix-suffix sweep + std::vector L(d + 1), R(d + 1); + L[0] = ITensor(1.0); + for (int i = 0; i < d; ++i) { + L[i + 1] = L[i] * (cores[i] * phi[i]); } - for(int k = 1; k <= d; ++k) { - // replace dimension k's basis vector with its derivative, keep all others unchanged - auto result = tt(1) * (k == 1 ? basisd_evals[0] : basis_evals[0]); - for(int i = 2; i <= d; ++i) { - result *= tt(i) * (k == i ? basisd_evals[i - 1] : basis_evals[i - 1]); - } - grad[k - 1] = elt(result); + R[d] = ITensor(1.0); + for (int i = d - 1; i >= 0; --i) { + R[i] = (cores[i] * phi[i]) * R[i + 1]; + } + + double val = elt(L[d]); + + // Gradient combination — independent across k + std::vector grad(d); + #pragma omp parallel for num_threads(nt) schedule(static) + for (int k = 0; k < d; ++k) { + grad[k] = elt(L[k] * (cores[k] * dphi[k]) * R[k + 1]); } - return grad; + + return {val, grad}; +} + +// ttEval delegates to ttEvalAndGrad and discards the gradient. +// Called infrequently (error measurement, well-tempered height) so the +// cost of computing dphi is negligible relative to avoiding code duplication. +double ttEval(const MPS& tt, + const std::vector& basis, + const std::vector& elements, + bool conv) { + return ttEvalAndGrad(tt, basis, elements, conv).first; } // Compute covariance matrix, marginal means, and partition function of the TT distribution. diff --git a/src/ttsketch/TTHelper.h b/src/ttsketch/TTHelper.h index a05007e1fb..04265d0efb 100644 --- a/src/ttsketch/TTHelper.h +++ b/src/ttsketch/TTHelper.h @@ -5,6 +5,7 @@ #ifdef __PLUMED_HAS_LIBITENSOR #ifdef __PLUMED_HAS_LIBHDF5 #include +#include namespace PLMD { namespace ttsketch { @@ -21,9 +22,6 @@ itensor::MPS ttSumRead(const std::string& filename, unsigned count); // Evaluate the TT bias at point `elements` by contracting each core with its // 1D basis vector. If conv=true, basis functions are evaluated in convolution mode. double ttEval(const itensor::MPS& tt, const std::vector& basis, const std::vector& elements, bool conv); -// Gradient of ttEval w.r.t. `elements`. Computed by replacing the k-th dimension's -// basis vector with its derivative while keeping all others unchanged (chain rule). -std::vector ttGrad(const itensor::MPS& tt, const std::vector& basis, const std::vector& elements, bool conv); // Compute the covariance matrix, mean vector, and partition function of the TT distribution. // Normalizes tt by Z = int tt(x) dx, then returns: // sigma(k,l) = E[x_k * x_l] - E[x_k]*E[x_l] (covariance matrix) @@ -34,7 +32,11 @@ std::tuple, std::vector, double> covMat(const itensor::MP // Fill `grid` (bins x bins) with the 2D marginal density of `tt` for dimensions // pos1 and pos2, obtained by integrating out all other dimensions analytically. void marginal2d(const itensor::MPS& tt, const std::vector& basis, int pos1, int pos2, Matrix& grid, bool conv); - +std::pair> + ttEvalAndGrad(const itensor::MPS& tt, + const std::vector& basis, + const std::vector& elements, + bool conv); } } #endif // __PLUMED_HAS_LIBHDF5 diff --git a/src/ttsketch/TTMetaD.cpp b/src/ttsketch/TTMetaD.cpp index 6238f80133..4b6c7eedc3 100644 --- a/src/ttsketch/TTMetaD.cpp +++ b/src/ttsketch/TTMetaD.cpp @@ -618,9 +618,13 @@ double TTMetaD::getBias(const std::vector& cv) { } double TTMetaD::getBiasAndDerivatives(const std::vector& cv, std::vector& der) { - double bias = length(this->vb_) == 0 ? 0.0 : ttEval(this->vb_, this->sketch_basis_, cv, this->sketch_conv_); - if(length(this->vb_) != 0) { - der = ttGrad(this->vb_, this->sketch_basis_, cv, this->sketch_conv_); + double bias = 0.0; + if (length(this->vb_) != 0) { + auto [tt_bias, tt_grad] = ttEvalAndGrad(this->vb_, this->sketch_basis_, cv, this->sketch_conv_); + bias = tt_bias; + der = std::move(tt_grad); + } else { + der.assign(this->d_, 0.0); } unsigned nt = OpenMP::getNumThreads(); if(this->hills_.size() < 2 * nt || nt == 1) {