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Fix remaining GeometryEngine issues #51

Merged
merged 57 commits into from
Dec 8, 2015
Merged

Fix remaining GeometryEngine issues #51

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a6b5636
replace rejection sampling with selection from precomputed values
Dec 1, 2015
8dbb9c1
fixing probability calculations
Dec 1, 2015
b11e958
moved old geometry engine to the attic
Dec 1, 2015
a1b3e69
add 1/2 prefactor
Dec 1, 2015
24ed133
calculate logZ separately
Dec 1, 2015
1bb11e4
fixed bond and angle proposals
Dec 2, 2015
48ffa76
make sure beta is in the right units
Dec 2, 2015
38ac293
fixed angle thing
Dec 2, 2015
1344f99
removed unused method
Dec 2, 2015
d2adbb6
calculate reverse torsion_logp
Dec 2, 2015
bd08b30
removed unnecessary imports
Dec 2, 2015
25aedf7
fixed some unit stuff
Dec 2, 2015
9346fff
remove loop
Dec 2, 2015
52aa9d2
remove another loop
Dec 2, 2015
cf92673
make jacobian optional again
Dec 2, 2015
ec3e218
prevent integer division
Dec 2, 2015
d8ee10e
make some fixes
Dec 2, 2015
9aa04c2
rename
Dec 2, 2015
6542577
cleaning up additional errors
Dec 2, 2015
a807260
added some explicit units
Dec 2, 2015
6a6fabc
subtracted max from logq
Dec 2, 2015
a741bf3
fix denominator
Dec 2, 2015
98e5673
fix units
Dec 2, 2015
cc32579
create functions to assign units properly
Dec 3, 2015
9032910
continue fixing unit errors
Dec 3, 2015
63fae74
fix more units...
Dec 3, 2015
045a1cb
removed superfluous units
Dec 3, 2015
f49a85e
still more units...
Dec 3, 2015
625aedb
don't add another set of units...
Dec 3, 2015
32bc181
corrected sign
Dec 3, 2015
74b8a6e
changed sum
Dec 3, 2015
5cac44b
fix unit mistake
Dec 3, 2015
e40e2a1
another unit mistake.
Dec 3, 2015
8d3e5c3
bond units
Dec 3, 2015
21a3182
fixed torsion units
Dec 3, 2015
bc78b1c
stop casting beta
Dec 3, 2015
8e2a426
fix some unit stuff
Dec 3, 2015
8f0db37
fix force constants
Dec 3, 2015
30cce16
replace -inf with exception
Dec 3, 2015
4f691a2
change logp calculation
Dec 3, 2015
e6bdbda
fixed torsion units
Dec 3, 2015
2998ccb
fix torsion selection
Dec 3, 2015
bc433e5
fix typo
Dec 3, 2015
c620e14
make unit-ing idempotent
Dec 3, 2015
2635d12
replace linspace with arange
Dec 4, 2015
df0eb21
fixed arange
Dec 4, 2015
1d16806
use more numerically stable cartesian to internal coordinate conversion
Dec 4, 2015
ca3f0ea
add coordinate conversion with units
Dec 6, 2015
73e137d
change parmtop input
Dec 6, 2015
0ba012b
fixes
Dec 7, 2015
806adc0
fix angles
Dec 8, 2015
d956d88
test angle computation
Dec 8, 2015
5ca5c9f
remove plotting
Dec 8, 2015
cba5b45
temprorary unit fix
Dec 8, 2015
390efd1
change name of test to make run
Dec 8, 2015
d465db1
calculate determinant of jacobian
Dec 8, 2015
6d5788e
fix unit
Dec 8, 2015
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