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proteneer / timemachine

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remove extraneous summed potential now that the L-E ixn groups are merged #1384

Closed jkausrelay closed 2 months ago

jkausrelay commented 2 months ago
proteneer commented 2 months ago

(this PR likely will block #1380 as well)

jkausrelay commented 2 months ago

Could you add benchmarks for this? Don't think this should make much of a difference, but may as we are no longer doing an additional event sync for the summed potential.

master:

dhfr-apo: N=23558 speed: 394.51ns/day dt: 2.5fs (ran 100000 steps in 54.94s)
dhfr-apo-barostat-interval-25: N=23558 speed: 317.31ns/day dt: 2.5fs (ran 100000 steps in 68.26s)
building a protein system with 1758 protein atoms and 7047 water atoms
Optimizing initial state at λ=0.1
----------------------------------------------------------------------
performing BFGS minimization on 265 atoms
(holding the other 8575 atoms frozen)
U(x_0) = -102393.346
Warning: Desired error not necessarily achieved due to precision loss.
         Current function value: -103237.889515
         Iterations: 361
         Function evaluations: 511
         Gradient evaluations: 495
U(x_final) = -103237.890
atom with highest force norm after minimization: 1117
force(x_final)[1117] = [-261.1905371    99.43120306  171.57122914]
----------------------------------------------------------------------
hif2a-apo: N=8805 speed: 701.40ns/day dt: 2.5fs (ran 100000 steps in 30.98s)
hif2a-apo-barostat-interval-25: N=8805 speed: 549.89ns/day dt: 2.5fs (ran 100000 steps in 39.47s)
hif2a-rbfe-barostat-interval-25: N=8840 speed: 505.52ns/day dt: 2.5fs (ran 100000 steps in 42.92s)
hif2a-rbfe-local: N=8840 speed: 1394.09ns/day dt: 2.5fs (ran 100000 steps in 15.68s)
hif2a-rbfe-barostat-interval-25-water-sampling-interval-400: N=8840 speed: 475.14ns/day dt: 2.5fs (ran 100000 steps in 45.66s)
Optimizing initial state at λ=0.1
----------------------------------------------------------------------
performing BFGS minimization on 199 atoms
(holding the other 6118 atoms frozen)
U(x_0) = -83324.835
Warning: Desired error not necessarily achieved due to precision loss.
         Current function value: -84115.276026
         Iterations: 435
         Function evaluations: 552
         Gradient evaluations: 541
U(x_final) = -84115.276
atom with highest force norm after minimization: 645
force(x_final)[645] = [ 232.67846235  -71.46603238 -425.10828159]
----------------------------------------------------------------------
solvent-apo: N=6282 speed: 1113.60ns/day dt: 2.5fs (ran 100000 steps in 19.58s)
solvent-apo-barostat-interval-25: N=6282 speed: 774.76ns/day dt: 2.5fs (ran 100000 steps in 28.07s)
solvent-rbfe-barostat-interval-25: N=6317 speed: 696.87ns/day dt: 2.5fs (ran 100000 steps in 31.19s)
solvent-rbfe-local: N=6317 speed: 1509.83ns/day dt: 2.5fs (ran 100000 steps in 14.49s)
ahfe-barostat-interval-15: N=6316 speed: 705.09ns/day dt: 2.5fs (ran 100000 steps in 30.83s)
ahfe-local: N=6316 speed: 1483.53ns/day dt: 2.5fs (ran 100000 steps in 14.82s)

PR 1384:

dhfr-apo: N=23558 speed: 400.13ns/day dt: 2.5fs (ran 100000 steps in 54.17s)
dhfr-apo-barostat-interval-25: N=23558 speed: 319.14ns/day dt: 2.5fs (ran 100000 steps in 67.87s)
building a protein system with 1758 protein atoms and 7047 water atoms
Optimizing initial state at λ=0.1
----------------------------------------------------------------------
performing BFGS minimization on 265 atoms
(holding the other 8575 atoms frozen)
U(x_0) = -102393.346
Warning: Desired error not necessarily achieved due to precision loss.
         Current function value: -103237.889515
         Iterations: 361
         Function evaluations: 511
         Gradient evaluations: 495
U(x_final) = -103237.890
atom with highest force norm after minimization: 1117
force(x_final)[1117] = [-261.1905371    99.43120306  171.57122914]
----------------------------------------------------------------------
hif2a-apo: N=8805 speed: 703.66ns/day dt: 2.5fs (ran 100000 steps in 30.88s)
^[[A
hif2a-apo-barostat-interval-25: N=8805 speed: 550.65ns/day dt: 2.5fs (ran 100000 steps in 39.42s)
hif2a-rbfe-barostat-interval-25: N=8840 speed: 505.45ns/day dt: 2.5fs (ran 100000 steps in 42.93s)
hif2a-rbfe-local: N=8840 speed: 1402.57ns/day dt: 2.5fs (ran 100000 steps in 15.59s)
hif2a-rbfe-barostat-interval-25-water-sampling-interval-400: N=8840 speed: 475.38ns/day dt: 2.5fs (ran 100000 steps in 45.65s)
Optimizing initial state at λ=0.1
----------------------------------------------------------------------
performing BFGS minimization on 199 atoms
(holding the other 6118 atoms frozen)
U(x_0) = -83324.835
Warning: Desired error not necessarily achieved due to precision loss.
         Current function value: -84115.276026
         Iterations: 435
         Function evaluations: 552
         Gradient evaluations: 541
U(x_final) = -84115.276
atom with highest force norm after minimization: 645
force(x_final)[645] = [ 232.67846235  -71.46603238 -425.10828159]
----------------------------------------------------------------------
solvent-apo: N=6282 speed: 1116.81ns/day dt: 2.5fs (ran 100000 steps in 19.52s)
solvent-apo-barostat-interval-25: N=6282 speed: 772.58ns/day dt: 2.5fs (ran 100000 steps in 28.15s)
solvent-rbfe-barostat-interval-25: N=6317 speed: 697.83ns/day dt: 2.5fs (ran 100000 steps in 31.15s)
solvent-rbfe-local: N=6317 speed: 1518.08ns/day dt: 2.5fs (ran 100000 steps in 14.41s)
ahfe-barostat-interval-15: N=6316 speed: 704.06ns/day dt: 2.5fs (ran 100000 steps in 30.87s)
ahfe-local: N=6316 speed: 1478.57ns/day dt: 2.5fs (ran 100000 steps in 14.79s)