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Fix build matrices
2019-08-22
B
erk He
s
s
Fi
x
p
erturbed
bon
d
ed bug
commit
|
commitdiff
|
tree
2019-08-20
Berk Hess
M
erge two dihedral function
s
commit
|
commitdiff
|
tree
2019-08-20
Berk Hess
U
s
e shif
t
Forces in ForceOuputs
commit
|
commitdiff
|
tree
2019-08-20
B
erk
H
ess
M
a
ke bond
e
d viri
a
l computa
t
i
on cond
i
tional
commit
|
commitdiff
|
tree
2019-08-20
Berk
Hess
F
i
x mis
s
i
n
g b
o
nded forces
w
ith CUDA
G
P
Us
a
n
d
DD
commit
|
commitdiff
|
tree
2019-08-15
Berk H
e
ss
Te
m
plate bo
n
ded inter
a
ctions on kern
e
l flav
o
r
commit
|
commitdiff
|
tree
2019-08-09
Ber
k
Hess
M
o
v
e
bon
d
ed
function table into bonded
.
cp
p
commit
|
commitdiff
|
tree
2019-08-09
B
e
r
k Hess
SIMD accelerat
i
on fo
r
F
_
FOUR
D
IH
S
a
nd F_PID
I
HS
commit
|
commitdiff
|
tree
2019-08-06
Berk Hes
s
Add ForceWithShiftForces class
commit
|
commitdiff
|
tree
2019-08-06
Berk He
s
s
F
i
x l
a
tex f
o
r
mula in r
e
ference manu
a
l
commit
|
commitdiff
|
tree
2019-08-05
B
erk Hess
Make box const in do_f
o
r
ce()
commit
|
commitdiff
|
tree
2019-08-05
B
e
rk Hess
Change ForceOutputs to a clas
s
commit
|
commitdiff
|
tree
2019-08-03
Berk Hess
Remov
e
s
emicolon
f
rom G
P
U
TERM macro
s
commit
|
commitdiff
|
tree
2019-08-02
B
e
rk Hess
Made gmx disre work wi
t
h non-consecutivel
y
labeled
.
.
.
commit
|
commitdiff
|
tree
2019-08-01
B
e
rk Hess
Re
m
ove a
pointer in t_f
o
r
cerec
commit
|
commitdiff
|
tree
2019-08-01
Berk H
e
s
s
Fix nbnxm GPU memory reserva
t
ion issue
commit
|
commitdiff
|
tree
2019-07-31
Berk
Hess
Remo
v
e unused CGL
O
_
INITIALIZAT
I
ON
commit
|
commitdiff
|
tree
2019-07-31
Be
r
k Hess
Remove vcm remova
l
from compute_globals()
commit
|
commitdiff
|
tree
2019-07-31
Ber
k
Hess
Ad
d
grompp warni
n
g with u
s
e of G
R
OMO
S
FF
commit
|
commitdiff
|
tree
2019-07-31
Berk H
e
s
s
Remove
n
eed for GROMOS FF in test
commit
|
commitdiff
|
tree
2019-07-30
Ber
k
Hes
s
Use invsqrt and cbr
t
in f
r
ee energy kernel
commit
|
commitdiff
|
tree
2019-07-29
B
erk Hes
s
Rem
o
ve LJ Ewald c
o
r
re
c
tion tables
commit
|
commitdiff
|
tree
2019-07-29
Berk Hess
Add initiali
z
a
t
i
on
t
o t_nrnb
commit
|
commitdiff
|
tree
2019-07-29
Berk He
s
s
Fix segm
e
nt
a
tion fault w
i
th cosine pulli
n
g
commit
|
commitdiff
|
tree
2019-07-28
Berk He
s
s
Removed g
e
neralized reaction-field
commit
|
commitdiff
|
tree
2019-07-28
Be
r
k Hess
C
o
nvert Ewald co
r
rect
i
on tables
to C++
commit
|
commitdiff
|
tree
2019-07-26
Berk Hess
Add de
f
ault ini
t
ializ
a
tion to interact
i
on_con
s
t_t
commit
|
commitdiff
|
tree
2019-07-26
Be
r
k
Hess
Remove sh_invrc6 from interactio
n
_
const_t
commit
|
commitdiff
|
tree
2019-07-25
Ber
k
H
e
ss
S
p
lit
c
a
nD
e
tectGpus()
commit
|
commitdiff
|
tree
2019-07-08
Ber
k
Hess
Sto
r
e
nbnxm
g
r
i
dSet d
a
t
a
in Grid
S
etData
commit
|
commitdiff
|
tree
2019-07-05
Berk Hess
Ch
a
nge af
f
i
n
ity e
n
um to enum class
commit
|
commitdiff
|
tree
2019-07-02
Ber
k
Hess
Refactor
t
hread aff
i
nit
y
checki
n
g
commit
|
commitdiff
|
tree
2019-07-02
Berk Hess
Re-enable affinity diagonos
t
ics wit
h
M
PI
commit
|
commitdiff
|
tree
2019-07-01
Berk Hess
F
i
x MP
I
deadlock
i
n a
f
finity setti
n
g
commit
|
commitdiff
|
tree
2019-07-01
B
e
rk Hes
s
Templa
t
e fr
e
e-energy kernel on differing coul/vdw s
o
ft
.
.
.
commit
|
commitdiff
|
tree
2019-06-26
Be
r
k
H
e
ss
Remove tabulation from fre
e
-ene
r
gy k
e
rnel
commit
|
commitdiff
|
tree
2019-06-20
Berk He
s
s
Remove unnecessar
y
#if GMX_MP
I
in pm
e
code
commit
|
commitdiff
|
tree
2019-06-20
Berk Hess
Template free-energy
kernel o
n
s
o
f
t-core
commit
|
commitdiff
|
tree
2019-06-19
B
e
rk Hess
Refactor PME
atom handling
commit
|
commitdiff
|
tree
2019-06-19
B
e
rk
Hess
Removed unused code paths in the NB FE ker
n
el
commit
|
commitdiff
|
tree
2019-06-18
Be
r
k Hess
Make forcerec c
o
n
s
t
i
n
d
i
spatc
h
N
onbondedKernel()
commit
|
commitdiff
|
tree
2019-06-17
Berk Hess
Simplify
GPU
nbn
x
m x conversion
commit
|
commitdiff
|
tree
2019-06-17
Berk Hess
Remove
unused nbnxm inclu
d
e files
commit
|
commitdiff
|
tree
2019-06-11
B
erk
H
e
s
s
Allow AWH geo
m
etry 'direction' to be periodic
commit
|
commitdiff
|
tree
2019-06-10
Berk He
s
s
Fi
x
gmx wh
a
m
w
i
t
h angle geometries
commit
|
commitdiff
|
tree
2019-06-05
Berk H
e
ss
Fix reference SIMD memory alignm
e
nt
commit
|
commitdiff
|
tree
2019-05-29
Berk Hess
Fix
mis
s
ing intermolecular intera
c
t
i
ons with DD
commit
|
commitdiff
|
tree
2019-05-27
Berk Hess
Work around gcc 7 avx512
bug
commit
|
commitdiff
|
tree
2019-05-23
B
e
rk Hess
Fix
SHAKE dH/dlambda contributions
commit
|
commitdiff
|
tree
2019-05-14
Berk Hess
Make all do_
f
o
rce_lo
w
lev
e
l() input con
s
t
commit
|
commitdiff
|
tree
2019-05-14
Berk Hess
Correct
u
ser guide postion
r
estraint
v
irial
commit
|
commitdiff
|
tree
2019-05-04
Berk Hess
R
emove PME exclusion correction
commit
|
commitdiff
|
tree
2019-05-03
Berk Hess
Rem
o
ved
non-existent AWH mdp opt
i
o
n
commit
|
commitdiff
|
tree
2019-05-03
Berk Hess
C
onvert manage_threading_t and gmx_enerdata_t to
C++
commit
|
commitdiff
|
tree
2019-05-02
B
e
rk Hess
Change nbnxm FE
P
p
o
inter
t
o unique_ptr
commit
|
commitdiff
|
tree
2019-04-30
Be
r
k Hess
Ad
d
con/de
s
t
ructor
f
or t_forcetable
commit
|
commitdiff
|
tree
2019-04-30
Berk Hess
Convert Di
s
persionCorrection to a class
commit
|
commitdiff
|
tree
2019-04-18
Ber
k
Hess
Remove nbnxm k
e
rn
e
l
t
ype from pairl
i
s
t
g
e
neration
commit
|
commitdiff
|
tree
2019-04-18
Berk
H
es
s
R
e
move cha
r
ge groups from domde
c
and localtop
commit
|
commitdiff
|
tree
2019-04-18
Berk Hess
Fix p
d
b-related iss
u
es
commit
|
commitdiff
|
tree
2019-04-17
B
e
rk Hess
Rem
o
ve gro
u
p sche
m
e
s
earch code
commit
|
commitdiff
|
tree
2019-04-17
B
er
k
Hess
Simplify vs
i
t
e
P
BC handling
commit
|
commitdiff
|
tree
2019-04-17
Berk
Hes
s
Red
u
ce nbn
x
m C
P
U
ke
r
nel
a
rg
u
ments
commit
|
commitdiff
|
tree
2019-04-17
Berk Hess
Simplify nbnx
m
shift
force ha
n
dling
commit
|
commitdiff
|
tree
2019-04-16
Ber
k
He
s
s
S
implify nbnxm buffer c
l
earing
commit
|
commitdiff
|
tree
2019-04-16
Berk Hess
Re
m
ove
RF_excl_cor
r
ection
(
)
commit
|
commitdiff
|
tree
2019-04-16
B
erk Hess
Make mdrun -nsteps work again
.
commit
|
commitdiff
|
tree
2019-04-15
B
erk Hess
Up
d
ate 20
1
9 release notes
f
o
r issue 2845
commit
|
commitdiff
|
tree
2019-04-15
Berk Hess
Fix pdb-related issu
e
s
commit
|
commitdiff
|
tree
2019-04-15
Berk Hess
Disallow pull geometry di
r
ec
t
ion-pe
r
iod
i
c with AWH
commit
|
commitdiff
|
tree
2019-03-28
Be
r
k Hess
Simplify nbnxm final force reduction
commit
|
commitdiff
|
tree
2019-03-28
Berk He
s
s
Move ea
r
ly return for nbnxm
force red
u
ction
commit
|
commitdiff
|
tree
2019-03-28
Berk Hess
Move PairlistSet
de
c
laration
commit
|
commitdiff
|
tree
2019-03-28
B
e
r
k Hess
Move nbnxm domainSetu
p
to GridSet
commit
|
commitdiff
|
tree
2019-03-28
Be
r
k H
e
s
s
E
x
tract nbnxm Pair
l
istS
e
ts
commit
|
commitdiff
|
tree
2019-03-27
Berk Hes
s
Fix nbnxm OpenCL with cluster siz
e
4
commit
|
commitdiff
|
tree
2019-03-25
Berk Hess
Convert nbnx
n
_pairl
i
s
t
_set_t to clas
s
PairlistSet
commit
|
commitdiff
|
tree
2019-03-20
Berk He
s
s
Move around PairSearch code
commit
|
commitdiff
|
tree
2019-03-19
B
e
rk Hes
s
Reduce dependencies of nbnxn_atomd
a
ta_
t
commit
|
commitdiff
|
tree
2019-03-15
Berk H
e
ss
Change nbnxn_s
e
a
rch to class PairSear
c
h
commit
|
commitdiff
|
tree
2019-03-15
Berk Hess
Extract DomainSetup f
r
om
nbnxn_search
commit
|
commitdiff
|
tree
2019-03-14
Berk Hess
Change
n
bnxm macros to
c
o
n
stexpr
commit
|
commitdiff
|
tree
2019-03-14
Berk H
e
ss
Move fu
n
ctions to gr
i
dset
.
cpp
commit
|
commitdiff
|
tree
2019-03-14
Be
r
k Hess
Add nbnxm GridSet clas
s
commit
|
commitdiff
|
tree
2019-03-14
Berk Hess
Fix
c
ompilatio
n
issue
commit
|
commitdiff
|
tree
2019-03-12
B
e
rk He
s
s
M
ove
n
b
nx
m
at
o
m
macros t
o
ato
m
data
.
h
commit
|
commitdiff
|
tree
2019-03-11
Berk Hess
Add grompp warn
i
ng with use of GROMOS FF
commit
|
commitdiff
|
tree
2019-03-08
Berk Hess
C
l
e
an up calc_verlet_buffer_size()
commit
|
commitdiff
|
tree
2019-03-06
B
erk H
e
ss
Clean up nbnxm boundin
g
box functions
commit
|
commitdiff
|
tree
2019-03-06
B
erk Hess
Clean up
nbnxm bou
n
d
i
ng boxes
commit
|
commitdiff
|
tree
2019-03-06
Berk Hess
Conv
e
rt nb
n
x
m
bounding
box to a struct
commit
|
commitdiff
|
tree
2019-03-05
Berk Hess
Fix post
-
submit warnings
commit
|
commitdiff
|
tree
2019-03-05
Berk Hess
M
o
ve
n
bnxm a
t
omdata types to atomdat
a
.
h
commit
|
commitdiff
|
tree
2019-03-05
Berk Hess
Turn nbn
x
n_
g
rid
_
t into a c
l
ass
commit
|
commitdiff
|
tree
2019-02-28
Berk Hes
s
Use
u
nique_ptr in nonbonded
_
verlet_t
commit
|
commitdiff
|
tree
2019-02-27
Berk Hess
U
s
e
n
ew/d
e
l
ete for t_f
o
rcerec
commit
|
commitdiff
|
tree
2019-02-27
Berk H
e
ss
Clean
up disp
e
rsioncor
r
ectio
n
.
cp
p
commit
|
commitdiff
|
tree
2019-02-27
B
erk Hess
Fix 4 compilers warni
n
gs
commit
|
commitdiff
|
tree
2019-02-27
Berk Hess
Coll
e
c
t dispersion correction code
commit
|
commitdiff
|
tree
2019-02-26
B
erk Hess
Correct grompp
index f
i
le error message
commit
|
commitdiff
|
tree
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