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Remove LaTeX file writing from gmx check
2018-09-14
Be
r
k Hess
Change gmx_mo
l
t
y
pe_t
.
ilis
t
to Interac
t
ionLists
commit
|
commitdiff
|
tree
2018-09-13
Berk Hes
s
Add C++ v
e
rsi
o
n of t_i
l
ist
commit
|
commitdiff
|
tree
2018-09-12
Berk Hes
s
Convert vsi
t
e struc
t
s to C++
commit
|
commitdiff
|
tree
2018-09-12
Berk Hess
Convert DD
gmx
_
re
v
erse_t
o
p_t to C
+
+
commit
|
commitdiff
|
tree
2018-08-29
Berk Hess
Refactor wall poten
t
ial calculation
commit
|
commitdiff
|
tree
2018-08-24
B
e
rk H
e
ss
Replace gmx_hash_
t
by HashedMap
commit
|
commitdiff
|
tree
2018-08-24
Berk Hess
Merge "Merge branc
h
release-2018"
commit
|
commitdiff
|
tree
2018-08-24
Berk Hess
Add
s
iz
e
opti
m
ization to Has
h
e
dMap
commit
|
commitdiff
|
tree
2018-08-24
Berk Hess
A
d
d t
e
s
ts for
H
ashedMap
commit
|
commitdiff
|
tree
2018-08-22
Berk Hess
Fix miss
i
ng i
n
t
eractions
w
i
th
GPU and D
D
commit
|
commitdiff
|
tree
2018-08-21
Berk Hess
Ensure
d
omains are
l
arge enough for at
o
m motion
commit
|
commitdiff
|
tree
2018-08-21
Berk H
e
ss
Fixed
mdru
n
segv with QM/MM ONI
O
M scheme
commit
|
commitdiff
|
tree
2018-08-20
Berk Hess
Refactor calc_
v
erlet_buffer_
s
ize(
)
commit
|
commitdiff
|
tree
2018-08-20
Berk
Hess
Remove compacting from DD r
e
dis
t
ribute
commit
|
commitdiff
|
tree
2018-08-20
Berk Hess
Fix Verlet buf
f
er esti
m
a
t
e
w
ith BD
commit
|
commitdiff
|
tree
2018-08-20
B
e
r
k
Hes
s
F
i
x
clang na
m
espa
c
e commen
t
w
a
rning
commit
|
commitdiff
|
tree
2018-08-20
Berk Hess
Fix asser
t
ion fail
u
re in
C
G
commit
|
commitdiff
|
tree
2018-08-20
B
erk
H
e
ss
Re
a
l
ly fix CG with
multip
l
e domains
commit
|
commitdiff
|
tree
2018-08-20
B
e
rk He
s
s
Ma
k
e gmx_ga2l
a
_t a proper class
commit
|
commitdiff
|
tree
2018-08-18
Berk H
e
ss
Add check for pull g
r
o
up PBC
t
o grompp
commit
|
commitdiff
|
tree
2018-08-17
Berk Hess
Make pull pbc atom use Loca
l
A
t
omSe
t
commit
|
commitdiff
|
tree
2018-07-18
Berk
H
ess
Apply local atom
s
ets
i
n pull
c
ode
commit
|
commitdiff
|
tree
2018-07-03
Berk Hess
C
o
nvert gmx_has
h
_t
t
o
C++
commit
|
commitdiff
|
tree
2018-07-03
B
erk Hes
s
Localize va
r
iables in dd_redis
t
r
i
b
u
te_cg()
commit
|
commitdiff
|
tree
2018-07-02
Berk Hes
s
C
o
nvert D
D
DLB cell s
i
ze handling to C++
commit
|
commitdiff
|
tree
2018-07-02
Berk Hess
Fix recent bug with
2D/3D DLB
commit
|
commitdiff
|
tree
2018-07-01
Berk
H
e
ss
Removed
s
malloc
.
h
fro
m
many DD
f
iles
commit
|
commitdiff
|
tree
2018-06-29
B
e
rk Hess
Co
n
ver
t
gmx_
d
omd
e
c_cons
t
r
aints_t to C+
+
commit
|
commitdiff
|
tree
2018-06-29
Berk Hess
Convert
gmx_domdec_specat_comm_t to C++
commit
|
commitdiff
|
tree
2018-06-29
Berk Hess
I
nitialize DD DLB var
i
able
commit
|
commitdiff
|
tree
2018-06-29
Berk
H
es
s
N
ew quote
fr
o
m a
r
eferee
commit
|
commitdiff
|
tree
2018-06-28
Ber
k
Hess
Renam
e
atomGro
u
p
s in gmx_domdec_t to atomGrouping
commit
|
commitdiff
|
tree
2018-06-28
B
e
r
k
H
ess
C
l
ean up
d
d
_
m
ove_cellx()
commit
|
commitdiff
|
tree
2018-06-28
Be
r
k Hess
C
o
nvert gmx_domd
e
c_sort_t to C++
commit
|
commitdiff
|
tree
2018-06-28
Berk Hess
Change B
l
ockRan
g
es to clas
s
Ra
n
gePartit
i
o
n
ing
commit
|
commitdiff
|
tree
2018-06-27
Berk Hess
Fix bu
g
with 2D/
3
D
tri
c
linic
DD
commit
|
commitdiff
|
tree
2018-06-27
Berk
Hess
Base
vacuum DD on a
t
om coordinates
commit
|
commitdiff
|
tree
2018-06-27
Ber
k
He
s
s
Add cons
i
stency check to DD
A
tomRanges
commit
|
commitdiff
|
tree
2018-06-27
Berk Hess
Pa
r
tial c
o
nversion of g
m
x_do
m
d
ec_c
o
mm
_
t to C++
commit
|
commitdiff
|
tree
2018-06-27
Berk
H
ess
T
em
p
late and overload dd_sendre
c
v functions
commit
|
commitdiff
|
tree
2018-06-27
Berk Hess
Correct DD zone size lo
o
p b
o
und
commit
|
commitdiff
|
tree
2018-06-14
Berk Hess
Min
i
m
i
zat
i
on now detects infinite forces
commit
|
commitdiff
|
tree
2018-06-14
Berk Hess
I
ntroduced
D
DA
t
omRang
e
s class
commit
|
commitdiff
|
tree
2018-06-13
Berk Hes
s
Rem
o
ve
L
INCS pr
i
nts to l
o
g
f
i
le
commit
|
commitdiff
|
tree
2018-06-13
B
erk
Hes
s
Par
t
ial conversion
of
g
mx_d
o
mdec_t to C++
commit
|
commitdiff
|
tree
2018-06-12
Ber
k
H
e
ss
Add AWH
c
ontinuation consis
t
en
c
y checking
commit
|
commitdiff
|
tree
2018-06-12
Berk Hess
Add fatal error for in
c
on
s
istent graph
commit
|
commitdiff
|
tree
2018-06-12
Berk He
s
s
Avoid
C
OM removal moving f
r
ozen a
t
oms
commit
|
commitdiff
|
tree
2018-06-12
B
erk
Hes
s
Remove constrai
n
t v
c
orrectio
n
f
o
r frozen atoms
commit
|
commitdiff
|
tree
2018-06-06
Berk Hess
Clean up make_at2
c
o
n
commit
|
commitdiff
|
tree
2018-06-06
Berk Hes
s
Fix MPI
i
nconsiste
n
cy
in EM after constraint failure
commit
|
commitdiff
|
tree
2018-06-05
Berk H
e
ss
Make nb
n
xn_grid_t counts and si
z
e
s arrays
commit
|
commitdiff
|
tree
2018-06-04
Berk Hess
Fix
s
egv in AWH
error message
commit
|
commitdiff
|
tree
2018-05-24
B
e
rk He
s
s
Fix gromp
p
bug
wi
t
h
blocks o
f
same molecules
commit
|
commitdiff
|
tree
2018-05-24
Berk
H
ess
Simpli
f
y ide
f
_fe in calc_list
e
d_lambda
commit
|
commitdiff
|
tree
2018-05-24
Berk Hess
Change n
b
s in nbv to std::u
n
ique
commit
|
commitdiff
|
tree
2018-05-24
B
erk
H
ess
C
o
n
vert gmx_domdec_master_t to C++
commit
|
commitdiff
|
tree
2018-05-23
Berk
H
e
s
s
Split off collect
.
cpp from d
o
m
d
ec
.
cp
p
commit
|
commitdiff
|
tree
2018-05-23
Berk Hess
Convert nbnxn_sea
r
ch to C++
commit
|
commitdiff
|
tree
2018-05-22
Berk He
s
s
C
hange nbnx
n
grid realloc
a
tion
commit
|
commitdiff
|
tree
2018-05-22
B
e
rk H
e
ss
Use std::vector in nbnx
n
_sear
c
h_t
commit
|
commitdiff
|
tree
2018-05-22
Berk Hess
Use std::vect
o
r
in
n
bnxn_g
r
id
_
t
commit
|
commitdiff
|
tree
2018-05-18
Berk Hess
C
l
ean up in
n
bnxn_
g
rid
.
c
pp
commit
|
commitdiff
|
tree
2018-05-17
Berk Hess
Spli
t
off domde
c
di
s
tribution a
n
d cellsizes
commit
|
commitdiff
|
tree
2018-05-17
Berk Hess
Spl
i
t atom
redistribution off
from
domd
e
c
.
c
p
p
commit
|
commitdiff
|
tree
2018-05-17
Berk Hes
s
Remove commrec from s
e
t_ddbox(
)
commit
|
commitdiff
|
tree
2018-05-15
Berk Hess
Clean up
PME d
o
main count passi
n
g
commit
|
commitdiff
|
tree
2018-05-03
Berk
H
ess
Enable SIMD version o
f
updat
e
commit
|
commitdiff
|
tree
2018-04-27
Berk Hes
s
Remove pull
M
PI code dupli
c
ation
commit
|
commitdiff
|
tree
2018-04-24
Berk He
s
s
Fix indexing issue i
n
the
p
ull code
commit
|
commitdiff
|
tree
2018-04-16
Berk Hess
Mo
v
e natoms_mol out o
f
gmx
_
molblock_t
commit
|
commitdiff
|
tree
2018-04-09
Berk Hes
s
Convert gmx_
m
olblock_t
t
o C++
commit
|
commitdiff
|
tree
2018-04-03
Ber
k
Hess
Convert
gmx_mtop
_
t to C++
commit
|
commitdiff
|
tree
2018-04-03
B
e
rk
H
es
s
Change warninp
f
ilenm to std::s
t
ring
commit
|
commitdiff
|
tree
2018-04-03
Berk Hess
Do n
o
t calc
u
late COM for pul
l
group
0
commit
|
commitdiff
|
tree
2018-03-29
Berk
H
es
s
Move
file opening o
u
t
of init
_
pull()
commit
|
commitdiff
|
tree
2018-03-29
Berk Hess
Modularize
p
ull_c
o
ord_wo
r
k_t
commit
|
commitdiff
|
tree
2018-03-28
Berk He
s
s
Remove
mo
l
s
from gmx_mtop_t
commit
|
commitdiff
|
tree
2018-03-20
Be
r
k Hess
Fix
gmx dump AWH formatting issu
e
commit
|
commitdiff
|
tree
2018-03-20
Be
r
k Hess
Disall
o
w
s
i
ngle simulati
o
n
wit
h
mu
l
tisim
commit
|
commitdiff
|
tree
2018-03-16
Berk Hes
s
Correct PMF sign error in
A
WH bias sharing
commit
|
commitdiff
|
tree
2018-03-16
Berk Hess
Fix recent md
r
un signa
l
ing bug
commit
|
commitdiff
|
tree
2018-03-15
Berk H
e
ss
F
i
x viria
l
wit
h
external pull potentia
l
and MPI
commit
|
commitdiff
|
tree
2018-03-14
Berk H
e
ss
Improve
inter-si
m
ulation s
i
gnalin
g
commit
|
commitdiff
|
tree
2018-03-14
Ber
k
Hess
Fix mdr
u
n s
i
g
n
a
l
ling w
i
th AW
H
b
i
a
s shari
n
g
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
Fix CO
M
pu
l
l
i
ng with ex
t
ernal potential
with
#
r
anks>32
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
Fi
x
pull bug with geome
t
ry=d
i
re
c
tion-
p
eri
o
dic
commit
|
commitdiff
|
tree
2018-03-13
Berk H
e
ss
Add AWH fixes t
o
r
el
e
ase not
e
s
commit
|
commitdiff
|
tree
2018-03-13
B
erk Hes
s
Fix AWH
e
nsemble checkpo
i
nt
i
ng
commit
|
commitdiff
|
tree
2018-03-13
Berk He
s
s
F
i
x
AWH deconvolution
w
hen sharing a b
i
as
commit
|
commitdiff
|
tree
2018-03-09
Berk Hess
Co
r
rect p
d
b2gmx
-
m
i
ssi
n
g op
t
ion
commit
|
commitdiff
|
tree
2018-03-07
B
erk Hess
Fix me
m
ory
lea
k
in PME
commit
|
commitdiff
|
tree
2018-03-06
Be
r
k Hess
Convert t
_
filenm to C++
commit
|
commitdiff
|
tree
2018-03-06
Berk Hess
M
a
k
e
multi-atom TPI reproducibl
e
commit
|
commitdiff
|
tree
2018-03-05
Berk Hess
Work
a
round gc
c
bug with group
k
e
rn
e
l tab
l
es
commit
|
commitdiff
|
tree
2018-03-05
Berk Hes
s
Leave
n
u
llptr opt in t_filenm
commit
|
commitdiff
|
tree
2018-03-02
B
erk
H
ess
Fix cpp
c
hec
k
warning
commit
|
commitdiff
|
tree
2018-03-02
Berk He
s
s
Fix AWH bias-sharing with parallel s
i
m
ulation
commit
|
commitdiff
|
tree
2018-03-01
Berk Hess
D
e
tect A
M
D SMT topology
commit
|
commitdiff
|
tree
2018-03-01
Berk Hess
Fix
mdrun mult
i
sim
with
s
eparate PM
E
r
anks
commit
|
commitdiff
|
tree
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