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Enable TPI with the Verlet cut-off scheme
2018-09-27
B
erk Hess
Move maxRe
f
e
r
en
c
e
T
emperature() to
i
nputrec
commit
|
commitdiff
|
tree
2018-09-27
Berk
H
e
ss
Improve update gro
u
p ra
d
ii
commit
|
commitdiff
|
tree
2018-09-27
Berk Hess
Reorganize RVec
scal
i
n
g
fu
n
ctions
commit
|
commitdiff
|
tree
2018-09-26
Berk Hes
s
Extract settle tes
t
wa
t
e
r
coordinates
commit
|
commitdiff
|
tree
2018-09-26
Berk Hess
Support atom gro
u
ps
in nbnxn_search
commit
|
commitdiff
|
tree
2018-09-25
Berk Hess
Add Upda
t
eGrou
p
s
C
og class
commit
|
commitdiff
|
tree
2018-09-24
Berk
H
ess
Fix
performance report when init_
s
tep!=0
commit
|
commitdiff
|
tree
2018-09-22
Berk Hess
Add u
p
da
t
e groups b
o
olean to DD
commit
|
commitdiff
|
tree
2018-09-22
B
e
rk
H
es
s
Ren
a
me D
D
constraint
b
ool
e
ans
commit
|
commitdiff
|
tree
2018-09-22
Berk Hess
A
dd update groups
commit
|
commitdiff
|
tree
2018-09-20
Berk Hess
Cha
n
ge
p
u
ll buffers
t
o std::vect
o
r
commit
|
commitdiff
|
tree
2018-09-20
B
e
rk Hess
Fix type
bug in
trili
n
ic DD code
commit
|
commitdiff
|
tree
2018-09-19
Berk He
s
s
C
onvert gmx_cmap_t
to C++
commit
|
commitdiff
|
tree
2018-09-19
Berk Hess
Convert
g
mx_ffparams_t to C++
commit
|
commitdiff
|
tree
2018-09-18
Berk Hess
Introduc
e
extractILists helper func
t
i
o
n
commit
|
commitdiff
|
tree
2018-09-18
Berk He
s
s
Re
f
actor ddbox
h
andling
commit
|
commitdiff
|
tree
2018-09-17
Berk H
e
ss
Move ifunc stuff f
r
om idef
.
h to ifunc
.
h
commit
|
commitdiff
|
tree
2018-09-17
Berk Hess
C
hange p
o
inters to Intera
c
tionList to references
commit
|
commitdiff
|
tree
2018-09-16
Ber
k
Hess
Refactoring
in
D
D re
d
istribute
commit
|
commitdiff
|
tree
2018-09-14
Be
r
k
Hes
s
Refactor
g
etAt
o
m
G
roupD
i
st
r
ibution(
)
commit
|
commitdiff
|
tree
2018-09-14
Berk He
s
s
C
h
a
nge gmx_m
o
l
type
_
t
.
ilist to I
n
teract
i
onLists
commit
|
commitdiff
|
tree
2018-09-13
Berk
H
ess
Ad
d
C
++ version
of
t_ilist
commit
|
commitdiff
|
tree
2018-09-12
Berk Hess
C
onv
e
rt
v
si
t
e structs to
C
++
commit
|
commitdiff
|
tree
2018-09-12
Ber
k
Hess
Conv
e
rt DD gmx_rev
e
rse_t
o
p_t to C+
+
commit
|
commitdiff
|
tree
2018-09-10
Berk
H
ess
F
i
x
PME forces with FE witho
u
t
pert
u
r
b
e
d
q/LJ
commit
|
commitdiff
|
tree
2018-08-29
Be
r
k Hess
Refactor
w
all p
o
tent
i
al calculation
commit
|
commitdiff
|
tree
2018-08-24
Berk
Hess
R
eplace gmx_hash_t
b
y Hashe
d
Map
commit
|
commitdiff
|
tree
2018-08-24
B
e
rk Hes
s
Merg
e
"Mer
g
e branc
h
releas
e
-
2
0
1
8
"
commit
|
commitdiff
|
tree
2018-08-24
Berk Hess
Add size optimization to HashedM
a
p
commit
|
commitdiff
|
tree
2018-08-24
B
e
rk Hess
Add tests for Has
h
edMap
commit
|
commitdiff
|
tree
2018-08-22
Berk He
s
s
Fix missin
g
int
e
ractions wit
h
GPU and DD
commit
|
commitdiff
|
tree
2018-08-21
Berk Hess
En
s
u
r
e
domai
n
s
a
r
e
l
ar
g
e
e
nough for a
t
om mo
t
io
n
commit
|
commitdiff
|
tree
2018-08-21
Berk Hess
Fixed
m
drun
s
egv with QM/MM ONI
O
M scheme
commit
|
commitdiff
|
tree
2018-08-20
Berk
H
ess
R
e
f
a
ctor calc_ver
l
et_bu
f
fer_size()
commit
|
commitdiff
|
tree
2018-08-20
Berk
Hess
Remove c
o
mpacting from DD re
d
i
s
t
r
ibute
commit
|
commitdiff
|
tree
2018-08-20
Berk Hess
Fix Verlet bu
f
fer estimate with BD
commit
|
commitdiff
|
tree
2018-08-20
Berk Hess
Fi
x
cl
a
ng namespace comment warning
commit
|
commitdiff
|
tree
2018-08-20
B
er
k
H
e
ss
Fix assertion
failure in CG
commit
|
commitdiff
|
tree
2018-08-20
Berk Hes
s
Really fix CG w
i
t
h multiple domains
commit
|
commitdiff
|
tree
2018-08-20
Ber
k
Hess
M
a
ke gmx_ga2la_t
a pr
o
pe
r
class
commit
|
commitdiff
|
tree
2018-08-18
B
erk Hess
Add check
for p
u
l
l
group
PBC to
g
rompp
commit
|
commitdiff
|
tree
2018-08-17
Berk Hess
Make pull pbc
a
tom use LocalAtomSet
commit
|
commitdiff
|
tree
2018-07-18
B
erk Hess
A
pply
local
a
tom sets in
p
ull code
commit
|
commitdiff
|
tree
2018-07-03
Berk Hess
Convert gmx_ha
s
h_t to C++
commit
|
commitdiff
|
tree
2018-07-03
B
e
r
k
Hess
Localize
v
a
riables in dd_redistribute_cg()
commit
|
commitdiff
|
tree
2018-07-02
B
e
rk He
s
s
Conv
e
rt DD
DLB cell size handling to C++
commit
|
commitdiff
|
tree
2018-07-02
B
e
rk Hess
F
i
x
re
c
ent
bug with 2D/3D
DLB
commit
|
commitdiff
|
tree
2018-07-01
Berk Hess
Rem
o
ved sma
l
loc
.
h from m
a
ny DD files
commit
|
commitdiff
|
tree
2018-06-29
Be
r
k
H
ess
C
o
nvert gmx_domdec_constraints_t to C++
commit
|
commitdiff
|
tree
2018-06-29
B
erk Hess
Co
n
vert gmx_domdec_specat_comm_t t
o
C++
commit
|
commitdiff
|
tree
2018-06-29
Berk Hess
I
n
i
tial
i
z
e DD
D
LB variable
commit
|
commitdiff
|
tree
2018-06-29
Be
r
k Hess
N
ew quote from a refere
e
commit
|
commitdiff
|
tree
2018-06-28
Berk Hess
Rename
atomG
r
oup
s
in gmx_domdec_t to at
o
mGrou
p
ing
commit
|
commitdiff
|
tree
2018-06-28
B
e
rk
H
e
s
s
Clea
n
up dd
_
move_cell
x
(
)
commit
|
commitdiff
|
tree
2018-06-28
Berk Hess
Convert gmx_domdec_sor
t
_t t
o
C++
commit
|
commitdiff
|
tree
2018-06-28
B
erk He
s
s
Ch
a
nge BlockRa
n
ges to class RangePartit
i
oning
commit
|
commitdiff
|
tree
2018-06-27
B
erk Hess
Fix bug with 2D/3D tri
c
l
i
nic DD
commit
|
commitdiff
|
tree
2018-06-27
Be
r
k Hess
Base vacuu
m
DD
on at
o
m coordinates
commit
|
commitdiff
|
tree
2018-06-27
Berk Hess
Add consistency
c
h
eck
t
o DDAtom
R
a
n
ges
commit
|
commitdiff
|
tree
2018-06-27
B
erk
Hess
Partial co
n
version
of gmx_domde
c
_comm_t to
C++
commit
|
commitdiff
|
tree
2018-06-27
Berk Hess
Template and
ove
r
load dd_sendrecv
functions
commit
|
commitdiff
|
tree
2018-06-27
Berk Hess
Corre
c
t DD zone size loop bound
commit
|
commitdiff
|
tree
2018-06-14
B
e
rk
H
ess
Minimiza
t
ion now detects in
f
in
i
te
f
orce
s
commit
|
commitdiff
|
tree
2018-06-14
B
e
rk H
e
ss
Intro
d
uced DDA
t
omRang
e
s class
commit
|
commitdiff
|
tree
2018-06-13
Berk
H
e
s
s
R
emo
v
e LINCS prin
t
s to
log file
commit
|
commitdiff
|
tree
2018-06-13
Berk Hess
Par
t
ial conv
e
rsion of g
m
x_domde
c
_t
t
o C+
+
commit
|
commitdiff
|
tree
2018-06-12
Berk H
e
ss
Add AWH continuation co
n
sistency chec
k
in
g
commit
|
commitdiff
|
tree
2018-06-12
B
erk He
s
s
Add fatal error fo
r
incon
s
iste
n
t graph
commit
|
commitdiff
|
tree
2018-06-12
Berk He
s
s
Avoid COM remova
l
moving
f
rozen atoms
commit
|
commitdiff
|
tree
2018-06-12
Berk Hes
s
Rem
o
ve constraint v correct
i
on for frozen atoms
commit
|
commitdiff
|
tree
2018-06-06
B
erk Hess
C
lean up make_at2con
commit
|
commitdiff
|
tree
2018-06-06
B
erk Hess
Fix MPI inc
o
nsis
t
ency in
E
M
aft
e
r co
n
str
a
int failure
commit
|
commitdiff
|
tree
2018-06-05
Ber
k
Hess
Make nb
n
xn_grid_t
c
ounts and sizes arrays
commit
|
commitdiff
|
tree
2018-06-04
Ber
k
H
e
ss
Fix
s
egv in AWH error mes
s
a
ge
commit
|
commitdiff
|
tree
2018-05-24
Berk Hess
Fix grompp
bug with blocks of same
m
olecule
s
commit
|
commitdiff
|
tree
2018-05-24
Be
r
k Hess
Simpl
i
fy id
e
f
_fe in calc_list
e
d_l
a
m
b
da
commit
|
commitdiff
|
tree
2018-05-24
Berk
Hess
Change nbs in nbv
to std::unique
commit
|
commitdiff
|
tree
2018-05-24
Berk
Hess
Convert gm
x
_domd
e
c_master_t to C+
+
commit
|
commitdiff
|
tree
2018-05-23
Berk Hess
Spl
i
t of
f
collect
.
cpp from d
o
m
d
ec
.
cpp
commit
|
commitdiff
|
tree
2018-05-23
Ber
k
Hess
Conver
t
nbnxn_search to C+
+
commit
|
commitdiff
|
tree
2018-05-22
Ber
k
Hess
C
h
ang
e
nbn
x
n grid
r
e
a
llo
c
ation
commit
|
commitdiff
|
tree
2018-05-22
Berk Hess
Use std::vecto
r
in nbnxn_search_t
commit
|
commitdiff
|
tree
2018-05-22
Berk Hess
Use s
t
d::vect
o
r
in nb
n
xn_g
r
i
d
_t
commit
|
commitdiff
|
tree
2018-05-18
Berk He
s
s
Cle
a
n
up in nbnxn_grid
.
cpp
commit
|
commitdiff
|
tree
2018-05-17
Berk Hes
s
Split off domdec distribution and cellsizes
commit
|
commitdiff
|
tree
2018-05-17
Berk Hess
Split atom
r
edi
s
tribution off from domdec
.
cpp
commit
|
commitdiff
|
tree
2018-05-17
B
erk Hess
R
e
move commrec from
s
e
t
_d
d
box()
commit
|
commitdiff
|
tree
2018-05-15
Berk Hess
C
lean up PME do
m
ain count passi
n
g
commit
|
commitdiff
|
tree
2018-05-03
B
e
rk H
e
ss
Enable S
I
MD version of update
commit
|
commitdiff
|
tree
2018-04-27
Berk Hess
Remove p
u
l
l
MPI code
duplication
commit
|
commitdiff
|
tree
2018-04-24
Ber
k
Hess
Fix indexin
g
issue in
the pull cod
e
commit
|
commitdiff
|
tree
2018-04-16
Ber
k
Hess
Move n
a
toms_mol ou
t
of gmx_mol
b
loc
k
_t
commit
|
commitdiff
|
tree
2018-04-09
Berk Hess
C
onvert
gmx_molbloc
k
_t to C++
commit
|
commitdiff
|
tree
2018-04-03
Berk
Hess
Conv
e
rt gmx_mto
p
_
t to
C
+
+
commit
|
commitdiff
|
tree
2018-04-03
Berk
Hess
Chan
g
e
w
arninp filenm to std::str
i
ng
commit
|
commitdiff
|
tree
2018-04-03
B
e
rk Hess
Do not
calcu
l
ate
COM for pull group 0
commit
|
commitdiff
|
tree
2018-03-29
Berk Hess
Move file openin
g
out o
f
init_pull(
)
commit
|
commitdiff
|
tree
2018-03-29
B
e
rk Hess
M
o
d
u
l
arize pull_coord_w
o
r
k
_
t
commit
|
commitdiff
|
tree
2018-03-28
B
e
rk Hess
Remove m
o
l
s
f
r
om gmx_
m
top_t
commit
|
commitdiff
|
tree
2018-03-20
Berk Hess
Fix gm
x
d
u
m
p A
W
H formatting issue
commit
|
commitdiff
|
tree
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