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Correct grompp nstexpanded/nstcalcenergy check
2018-10-31
Berk Hes
s
Correct grompp n
s
t
expanded/nstcalcene
r
gy check
commit
|
commitdiff
|
tree
2018-10-26
Berk
H
ess
Add missing mass term
t
o
d
eltaH
commit
|
commitdiff
|
tree
2018-10-23
Be
r
k Hess
Add missing constraint
t
erm t
o
de
l
taH
commit
|
commitdiff
|
tree
2018-10-21
Berk H
e
ss
Fix mdrun
s
tart/end
t
i
m
e
p
rint
commit
|
commitdiff
|
tree
2018-10-18
B
e
r
k Hes
s
Add
en
v
.
var
.
to di
s
ab
l
e update grou
p
s
commit
|
commitdiff
|
tree
2018-10-12
B
e
rk H
e
ss
Imp
l
ement assigning bondeds
t
o th
e
GPU
commit
|
commitdiff
|
tree
2018-10-10
Berk Hess
Move
pull output
functio
n
s to out
p
ut
.
cpp
commit
|
commitdiff
|
tree
2018-10-10
Berk
Hess
M
i
n
or re
f
actori
n
g in b
o
nde
d
threading
commit
|
commitdiff
|
tree
2018-10-09
Berk Hess
Fi
x
comp
i
ler
w
arnin
g
commit
|
commitdiff
|
tree
2018-10-08
Be
r
k Hess
Enable
u
pd
a
te g
r
oups
commit
|
commitdiff
|
tree
2018-10-05
Berk
H
e
s
s
A
d
d
update groups to
D
D atom displacement
commit
|
commitdiff
|
tree
2018-10-04
B
erk Hess
M
a
ke AVX2 pass TSAN
commit
|
commitdiff
|
tree
2018-10-04
Berk Hess
Add note to avoid co
n
s
t
raint
s
=all-bo
n
ds
commit
|
commitdiff
|
tree
2018-10-03
Berk Hess
Remove unnece
s
sary clearing
i
n
gm
x
cpp
commit
|
commitdiff
|
tree
2018-10-03
Berk Hess
C
o
n
vert
gmx_
c
pp to C++
commit
|
commitdiff
|
tree
2018-10-02
B
e
rk
H
ess
Update DD c
u
t
o
ffs for update
g
r
oups
commit
|
commitdiff
|
tree
2018-09-30
Berk Hess
Correct
u
p
d
ate group angl
e
param type
commit
|
commitdiff
|
tree
2018-09-29
Berk Hess
Refa
c
toring i
n
calc_verletbuf
.
cpp
commit
|
commitdiff
|
tree
2018-09-29
Berk Hess
Add UpdateGroups
C
og
to DD
commit
|
commitdiff
|
tree
2018-09-27
Berk Hess
Move maxR
e
feren
c
eTemp
e
r
ature() to inputrec
commit
|
commitdiff
|
tree
2018-09-27
Berk Hes
s
Improve update grou
p
radii
commit
|
commitdiff
|
tree
2018-09-27
Ber
k
Hess
Reor
g
aniz
e
RVec scaling funct
i
ons
commit
|
commitdiff
|
tree
2018-09-26
Berk Hess
E
x
t
r
act sett
l
e test water coordinates
commit
|
commitdiff
|
tree
2018-09-26
Ber
k
Hess
Sup
p
ort atom group
s
in nb
n
xn
_
search
commit
|
commitdiff
|
tree
2018-09-25
B
e
r
k
Hess
A
d
d UpdateG
r
oupsCog class
commit
|
commitdiff
|
tree
2018-09-24
Berk H
e
ss
Fix perform
a
nce re
p
ort when init_step!=0
commit
|
commitdiff
|
tree
2018-09-22
Be
r
k
Hess
Add update group
s
b
ool
e
an to DD
commit
|
commitdiff
|
tree
2018-09-22
Berk Hes
s
Rename DD
c
o
ns
t
raint boolean
s
commit
|
commitdiff
|
tree
2018-09-22
B
e
rk Hess
A
d
d update gro
u
ps
commit
|
commitdiff
|
tree
2018-09-20
Berk Hess
Ch
a
nge p
u
ll buffers
to
std::vector
commit
|
commitdiff
|
tree
2018-09-20
Berk Hess
F
i
x type bu
g
in
tril
i
nic
DD code
commit
|
commitdiff
|
tree
2018-09-19
B
e
r
k
Hess
C
on
v
ert gmx_cmap_t
t
o C++
commit
|
commitdiff
|
tree
2018-09-19
Berk Hess
C
o
n
v
ert gmx_ffparams
_
t to
C
+
+
commit
|
commitdiff
|
tree
2018-09-18
B
erk He
s
s
Intro
d
uce e
x
trac
t
ILists helpe
r
functio
n
commit
|
commitdiff
|
tree
2018-09-18
Berk Hes
s
Refactor ddbo
x
handling
commit
|
commitdiff
|
tree
2018-09-17
Berk Hess
Move ifu
n
c stuff from i
d
ef
.
h
t
o ifu
n
c
.
h
commit
|
commitdiff
|
tree
2018-09-17
Ber
k
Hess
Chang
e
poi
n
t
ers to
Inte
r
act
i
onList to refere
n
ces
commit
|
commitdiff
|
tree
2018-09-16
Berk Hess
Ref
a
ctoring
i
n DD redistr
i
bute
commit
|
commitdiff
|
tree
2018-09-14
Berk Hess
R
e
factor getAtomG
r
oup
D
i
stribut
i
on()
commit
|
commitdiff
|
tree
2018-09-14
B
erk He
s
s
Change g
m
x
_molt
y
pe_t
.
ilist to
I
nt
e
r
a
cti
o
nL
i
sts
commit
|
commitdiff
|
tree
2018-09-13
B
e
r
k H
e
ss
Add C++ version of
t
_
i
l
ist
commit
|
commitdiff
|
tree
2018-09-12
Berk
Hess
Convert vsite
stru
c
t
s
to C++
commit
|
commitdiff
|
tree
2018-09-12
Berk Hess
Convert D
D
gmx_reverse_top_t to C++
commit
|
commitdiff
|
tree
2018-09-10
Berk Hess
Fix
P
ME forces with FE wit
h
out perturbed q/LJ
commit
|
commitdiff
|
tree
2018-08-29
B
erk Hess
Refa
c
tor
wall potential calculation
commit
|
commitdiff
|
tree
2018-08-24
B
erk
H
e
s
s
Replace gmx_hash_t by
HashedMap
commit
|
commitdiff
|
tree
2018-08-24
Berk Hess
Merge "Merge
b
r
an
c
h release-
2
018"
commit
|
commitdiff
|
tree
2018-08-24
Berk Hess
A
d
d size optimization
to HashedMap
commit
|
commitdiff
|
tree
2018-08-24
Berk He
s
s
Add tests
f
or HashedM
a
p
commit
|
commitdiff
|
tree
2018-08-22
Berk H
e
s
s
Fix mi
s
sing i
n
teractions with GP
U
an
d
DD
commit
|
commitdiff
|
tree
2018-08-21
Berk Hess
Ensu
r
e d
o
main
s
are large en
o
ugh for
a
t
om m
o
tion
commit
|
commitdiff
|
tree
2018-08-21
Ber
k
Hess
F
i
xed
mdr
u
n segv w
i
th QM/MM O
N
IO
M
sch
e
me
commit
|
commitdiff
|
tree
2018-08-20
B
e
rk Hess
Re
f
actor calc
_
v
e
r
let_
b
uffer_size(
)
commit
|
commitdiff
|
tree
2018-08-20
Berk Hess
Remove compacting from DD redistribute
commit
|
commitdiff
|
tree
2018-08-20
Berk Hess
Fix Verlet buffer estimate wit
h
BD
commit
|
commitdiff
|
tree
2018-08-20
Berk Hess
Fix clan
g
namespace
c
omment warning
commit
|
commitdiff
|
tree
2018-08-20
Berk Hess
Fix
a
ssertion fa
i
lur
e
i
n
C
G
commit
|
commitdiff
|
tree
2018-08-20
B
erk Hess
Real
l
y
f
ix CG with m
u
lti
p
le domains
commit
|
commitdiff
|
tree
2018-08-20
Be
r
k
H
e
ss
Make gmx_g
a
2la_t a proper
c
lass
commit
|
commitdiff
|
tree
2018-08-18
Berk H
e
ss
Add
c
he
c
k
for pul
l
g
r
oup
P
BC to
g
rompp
commit
|
commitdiff
|
tree
2018-08-17
B
e
rk He
s
s
Make pull
pbc
a
tom use
Loca
l
AtomSet
commit
|
commitdiff
|
tree
2018-07-18
Berk Hess
A
p
ply local at
o
m sets
in pull
c
o
de
commit
|
commitdiff
|
tree
2018-07-03
Berk H
e
ss
Co
n
vert gmx_hash_t to C++
commit
|
commitdiff
|
tree
2018-07-03
Berk H
e
s
s
Localiz
e
var
i
ables in dd_redistri
b
ute_cg()
commit
|
commitdiff
|
tree
2018-07-02
Berk Hess
Convert DD DLB cell size handlin
g
to C
+
+
commit
|
commitdiff
|
tree
2018-07-02
Be
r
k Hess
Fix recent bug with 2D/3D DLB
commit
|
commitdiff
|
tree
2018-07-01
Berk Hess
R
emoved sma
l
loc
.
h from
m
an
y
DD fi
l
es
commit
|
commitdiff
|
tree
2018-06-29
Berk Hess
Con
v
ert g
m
x_domdec_con
s
traints_t to C++
commit
|
commitdiff
|
tree
2018-06-29
Berk Hess
Convert gmx_domd
e
c_specat_
c
omm_t t
o
C++
commit
|
commitdiff
|
tree
2018-06-29
Berk He
s
s
Initi
a
lize DD DLB v
a
riable
commit
|
commitdiff
|
tree
2018-06-29
Berk He
s
s
New qu
o
te fro
m
a r
e
f
e
r
ee
commit
|
commitdiff
|
tree
2018-06-28
Berk He
s
s
Ren
a
me atom
G
roups
in
gmx_domdec_t to atom
G
roup
i
n
g
commit
|
commitdiff
|
tree
2018-06-28
B
e
r
k
Hess
Clean up
dd_move_
c
ellx()
commit
|
commitdiff
|
tree
2018-06-28
Berk H
e
ss
Con
v
er
t
gmx_domde
c
_sort_t to
C++
commit
|
commitdiff
|
tree
2018-06-28
B
erk H
e
ss
Change BlockRan
g
es to class RangeP
a
rtitioning
commit
|
commitdiff
|
tree
2018-06-27
Berk Hess
Fix bug with 2D/
3
D tr
i
cli
n
ic DD
commit
|
commitdiff
|
tree
2018-06-27
Berk He
s
s
Base vacuum D
D
on a
t
om co
o
r
dinates
commit
|
commitdiff
|
tree
2018-06-27
Be
r
k Hess
Add consistency check t
o
D
DAtomRanges
commit
|
commitdiff
|
tree
2018-06-27
Berk Hess
P
artial conversion of gm
x
_domde
c
_c
o
mm_t to C++
commit
|
commitdiff
|
tree
2018-06-27
Berk Hes
s
Templat
e
and ove
r
load dd_se
n
dre
c
v functio
n
s
commit
|
commitdiff
|
tree
2018-06-27
Berk Hes
s
Correct D
D
zone size
loop
b
o
u
n
d
commit
|
commitdiff
|
tree
2018-06-14
Berk Hess
Minimiza
t
ion
n
ow d
e
t
e
cts infin
i
te for
c
es
commit
|
commitdiff
|
tree
2018-06-14
Be
r
k Hess
Introduced DDAtomRanges cla
s
s
commit
|
commitdiff
|
tree
2018-06-13
Berk Hess
Remove LINCS pri
n
ts to log file
commit
|
commitdiff
|
tree
2018-06-13
Berk Hess
Pa
r
t
ia
l
co
n
versio
n
o
f
gmx_domdec_t to C++
commit
|
commitdiff
|
tree
2018-06-12
Berk Hes
s
A
dd AWH
c
o
n
tin
u
ation consistency ch
e
c
k
ing
commit
|
commitdiff
|
tree
2018-06-12
Berk Hess
Add fatal error for
inconsis
t
ent g
r
aph
commit
|
commitdiff
|
tree
2018-06-12
B
e
rk Hess
Av
o
id COM removal movi
n
g frozen ato
m
s
commit
|
commitdiff
|
tree
2018-06-12
B
er
k
Hess
Remo
v
e
c
onstraint v correction
f
or
f
rozen at
o
ms
commit
|
commitdiff
|
tree
2018-06-06
Be
r
k Hess
Clean
up make_at2co
n
commit
|
commitdiff
|
tree
2018-06-06
Berk Hess
Fix MPI
inconsistency in E
M
after cons
t
ra
i
nt
failure
commit
|
commitdiff
|
tree
2018-06-05
B
e
r
k Hess
Make nbn
x
n_grid_t
counts and siz
e
s ar
r
ays
commit
|
commitdiff
|
tree
2018-06-04
Ber
k
H
ess
Fix segv in AWH error message
commit
|
commitdiff
|
tree
2018-05-24
Berk Hess
Fix grompp bug
wi
t
h blocks of same mo
l
ecules
commit
|
commitdiff
|
tree
2018-05-24
Berk H
e
ss
S
implify
idef_fe in calc_li
s
ted_lambda
commit
|
commitdiff
|
tree
2018-05-24
Berk He
s
s
Cha
n
g
e
nbs i
n
nbv to std::unique
commit
|
commitdiff
|
tree
2018-05-24
B
e
rk Hess
Co
n
vert gmx_do
m
dec_master_t to C++
commit
|
commitdiff
|
tree
2018-05-23
Ber
k
Hess
Split off collect
.
cpp from domdec
.
cpp
commit
|
commitdiff
|
tree
2018-05-23
B
e
r
k H
e
ss
Convert nbnxn_search to C++
commit
|
commitdiff
|
tree
2018-05-22
Berk
Hess
Change nbn
x
n grid rea
l
location
commit
|
commitdiff
|
tree
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