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Remove gmx custom fixed int (e.g. gmx_int64_t) types
2018-07-18
Berk
Hess
Apply local ato
m
sets in pull co
d
e
commit
|
commitdiff
|
tree
2018-07-03
Berk Hess
Con
v
ert g
m
x_
h
ash_t to
C
+
+
commit
|
commitdiff
|
tree
2018-07-03
Berk
Hess
Localize variables
in dd_redistribute_cg()
commit
|
commitdiff
|
tree
2018-07-02
Berk H
e
ss
Convert
D
D
D
LB cell size handling to C++
commit
|
commitdiff
|
tree
2018-07-02
Berk Hess
F
i
x recen
t
b
u
g with 2D/3D DLB
commit
|
commitdiff
|
tree
2018-07-01
Berk Hess
Rem
o
v
e
d
s
malloc
.
h fro
m
many DD fil
e
s
commit
|
commitdiff
|
tree
2018-06-29
Be
r
k Hess
C
on
v
ert gmx
_
d
o
mdec_
c
ons
t
ra
i
nts_t to C++
commit
|
commitdiff
|
tree
2018-06-29
Berk Hess
Convert gm
x
_d
o
mdec_specat_comm
_
t
to
C
+
+
commit
|
commitdiff
|
tree
2018-06-29
B
erk H
e
ss
Initialize DD
DLB variable
commit
|
commitdiff
|
tree
2018-06-29
Berk Hess
New quote from
a ref
e
ree
commit
|
commitdiff
|
tree
2018-06-28
Berk Hess
Rename a
t
om
G
roups in gm
x
_d
o
m
d
e
c_t to atomGr
o
uping
commit
|
commitdiff
|
tree
2018-06-28
B
erk
Hess
Cl
e
an up dd_mo
v
e_cell
x
()
commit
|
commitdiff
|
tree
2018-06-28
Berk He
s
s
Convert
gmx_dom
d
ec_sort_t to
C
+
+
commit
|
commitdiff
|
tree
2018-06-28
Berk Hess
C
h
ange BlockRanges to class RangePa
r
titioning
commit
|
commitdiff
|
tree
2018-06-27
Berk Hess
Fix bug with 2D
/
3D
t
ricl
i
nic DD
commit
|
commitdiff
|
tree
2018-06-27
Berk Hess
B
ase vacuum
D
D on atom coordi
n
ates
commit
|
commitdiff
|
tree
2018-06-27
Ber
k
Hes
s
Add consistency ch
e
ck t
o
D
D
A
tomR
a
n
ges
commit
|
commitdiff
|
tree
2018-06-27
Be
r
k Hess
Partial co
n
version o
f
g
m
x_domdec
_
comm_t to C
+
+
commit
|
commitdiff
|
tree
2018-06-27
Berk Hess
Template and overload dd_sendrec
v
functi
o
ns
commit
|
commitdiff
|
tree
2018-06-27
Berk Hess
C
o
rrect D
D
zone siz
e
loop
bou
n
d
commit
|
commitdiff
|
tree
2018-06-14
Be
r
k
H
ess
Minimiza
t
ion now det
e
cts infin
i
te forces
commit
|
commitdiff
|
tree
2018-06-14
Berk Hes
s
Introdu
c
e
d DDAt
o
mRanges class
commit
|
commitdiff
|
tree
2018-06-13
Berk Hess
Re
m
o
v
e LINCS prints to
l
og
file
commit
|
commitdiff
|
tree
2018-06-13
Berk Hess
Par
t
i
a
l c
o
n
ver
s
ion of gm
x
_domdec_t to C++
commit
|
commitdiff
|
tree
2018-06-12
Berk Hess
Add A
W
H conti
n
uation consiste
n
cy che
c
king
commit
|
commitdiff
|
tree
2018-06-12
Be
r
k
Hess
Add fatal error for i
n
consis
t
ent graph
commit
|
commitdiff
|
tree
2018-06-12
Berk Hess
Avoid COM removal mov
i
ng fro
z
en atoms
commit
|
commitdiff
|
tree
2018-06-12
Berk Hess
Remove constr
a
int v correcti
o
n for frozen atoms
commit
|
commitdiff
|
tree
2018-06-06
Berk H
e
s
s
C
l
ean up make_at2con
commit
|
commitdiff
|
tree
2018-06-06
Berk Hess
Fix MPI inconsiste
n
cy in EM after co
n
strai
n
t failure
commit
|
commitdiff
|
tree
2018-06-05
Berk H
e
ss
Make nbnxn_grid_
t
counts
and sizes array
s
commit
|
commitdiff
|
tree
2018-06-04
Berk Hess
Fix
segv in
AW
H
e
rror
mes
s
a
ge
commit
|
commitdiff
|
tree
2018-05-24
Be
r
k
H
ess
Fix grompp b
u
g with
blocks of sa
m
e m
o
l
ecules
commit
|
commitdiff
|
tree
2018-05-24
Berk
H
e
ss
Simpl
i
fy ide
f
_fe in calc_listed_lambd
a
commit
|
commitdiff
|
tree
2018-05-24
Berk Hess
Change
nbs in nbv t
o
std:
:
unique
commit
|
commitdiff
|
tree
2018-05-24
Berk He
s
s
Convert gmx_domdec
_
master_t to
C
+
+
commit
|
commitdiff
|
tree
2018-05-23
Berk Hes
s
S
p
li
t
off colle
c
t
.
cpp from do
m
dec
.
cpp
commit
|
commitdiff
|
tree
2018-05-23
Berk Hess
Convert
n
b
nxn_searc
h
t
o C++
commit
|
commitdiff
|
tree
2018-05-22
Berk Hess
Chan
g
e nbnxn
g
r
id rea
l
lo
c
at
i
on
commit
|
commitdiff
|
tree
2018-05-22
Berk Hess
Use s
t
d:
:
v
e
ctor in nbnxn_search
_
t
commit
|
commitdiff
|
tree
2018-05-22
Berk
H
ess
Use std::v
e
ctor in nbnxn
_
grid
_
t
commit
|
commitdiff
|
tree
2018-05-18
Ber
k
Hess
C
l
ean up in nbnxn_grid
.
cpp
commit
|
commitdiff
|
tree
2018-05-17
Berk Hess
S
plit off domdec dis
t
ribut
i
on and ce
l
lsizes
commit
|
commitdiff
|
tree
2018-05-17
B
erk Hess
Split atom redistribution of
f
from domde
c
.
cp
p
commit
|
commitdiff
|
tree
2018-05-17
Berk
Hess
Remove co
m
m
rec from
s
et_dd
b
ox(
)
commit
|
commitdiff
|
tree
2018-05-15
Berk Hess
Clean u
p
PME domain
c
ount pas
s
ing
commit
|
commitdiff
|
tree
2018-05-03
Berk Hess
Ena
b
le
S
IMD ver
s
ion
of up
d
a
t
e
commit
|
commitdiff
|
tree
2018-04-27
B
e
rk
H
ess
Remove
pull MPI code du
p
lic
a
tion
commit
|
commitdiff
|
tree
2018-04-24
Berk Hess
Fix in
d
exing issue in the pull code
commit
|
commitdiff
|
tree
2018-04-16
Berk Hess
Move na
t
oms_mol out
o
f gmx_molblo
c
k
_t
commit
|
commitdiff
|
tree
2018-04-09
Berk Hess
Co
n
vert
g
mx_molbloc
k
_t
t
o C++
commit
|
commitdiff
|
tree
2018-04-03
Be
r
k Hess
Con
v
er
t
gmx_mtop_
t
to C++
commit
|
commitdiff
|
tree
2018-04-03
Ber
k
Hess
C
hange warninp filenm to st
d
:
:
string
commit
|
commitdiff
|
tree
2018-04-03
Berk Hess
Do not calculate COM for pull group 0
commit
|
commitdiff
|
tree
2018-03-29
Be
r
k
H
ess
M
ove fil
e
opening out of
i
nit_pull()
commit
|
commitdiff
|
tree
2018-03-29
Be
r
k Hes
s
M
o
du
l
arize pull_coor
d
_work_t
commit
|
commitdiff
|
tree
2018-03-28
Berk Hess
Rem
o
ve
m
ols fro
m
g
mx_m
t
op_t
commit
|
commitdiff
|
tree
2018-03-20
Berk Hess
F
ix gmx dump AWH formatting
issue
commit
|
commitdiff
|
tree
2018-03-20
Be
r
k
H
e
s
s
Disallow
s
ingle simul
a
tion with multisim
commit
|
commitdiff
|
tree
2018-03-16
Berk
H
ess
C
orrect P
M
F sign error
in AWH bi
a
s sharing
commit
|
commitdiff
|
tree
2018-03-16
Berk
H
ess
Fix
r
ecent mdrun
s
ignaling bug
commit
|
commitdiff
|
tree
2018-03-15
Berk Hes
s
Fix virial with external
p
ull potential
a
n
d
M
PI
commit
|
commitdiff
|
tree
2018-03-14
Berk Hes
s
Improve
inter-sim
u
lation s
i
gn
a
ling
commit
|
commitdiff
|
tree
2018-03-14
B
er
k
Hess
Fix mdru
n
sig
n
alling with
A
WH bias
s
harin
g
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
Fix COM pulling wit
h
externa
l
potential
with #ra
n
ks>32
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
Fix pul
l
bug
w
ith
g
eometry=dire
c
tion-
p
e
riod
i
c
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Add AWH fixes to
r
elease note
s
commit
|
commitdiff
|
tree
2018-03-13
Berk H
e
s
s
Fix AWH
e
n
semble
checkpoint
i
ng
commit
|
commitdiff
|
tree
2018-03-13
B
erk Hess
F
ix AWH deconvol
u
tion when
s
haring a bias
commit
|
commitdiff
|
tree
2018-03-09
Ber
k
He
s
s
Cor
r
ec
t
pdb2
g
mx
-
missing opti
o
n
commit
|
commitdiff
|
tree
2018-03-07
Berk
H
ess
Fix memo
r
y
le
a
k
in PME
commit
|
commitdiff
|
tree
2018-03-06
Berk Hess
Convert t
_
filenm
t
o C++
commit
|
commitdiff
|
tree
2018-03-06
Be
r
k Hess
M
ake multi-atom TPI rep
r
od
u
cible
commit
|
commitdiff
|
tree
2018-03-05
Berk He
s
s
Work around g
c
c
b
ug with
group
k
ernel ta
b
les
commit
|
commitdiff
|
tree
2018-03-05
Ber
k
Hess
Le
a
ve nullptr opt in t
_
filenm
commit
|
commitdiff
|
tree
2018-03-02
Berk Hess
F
ix cppch
e
ck warning
commit
|
commitdiff
|
tree
2018-03-02
Berk Hess
Fix AW
H
bias-shari
n
g with
p
ar
a
llel simu
l
at
i
on
commit
|
commitdiff
|
tree
2018-03-01
Berk Hess
Detect
AMD
S
M
T topology
commit
|
commitdiff
|
tree
2018-03-01
Berk Hess
Fix mdrun multisim with s
e
p
a
rat
e
P
ME ranks
commit
|
commitdiff
|
tree
2018-02-23
Berk Hess
Fix md integrator with
Nose
-
H
oover coupling
commit
|
commitdiff
|
tree
2018-02-22
Berk Hess
Simplify mdrun tMPI th
r
ead spawning
commit
|
commitdiff
|
tree
2018-02-16
Berk
H
e
s
s
Correct multisim MPI barrier
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Remove support
fo
r
tpx version befo
r
e 58/gm
x
4
.
0
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
F
i
x
r
ang
e
bug
i
n add
_
sel
e
ction_g
r
o
ups in tngio
.
cpp
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Fix grom
p
p net charge check
commit
|
commitdiff
|
tree
2018-02-14
Ber
k
Hess
Fix grompp n
e
t
c
harge c
h
e
c
k
commit
|
commitdiff
|
tree
2018-02-08
B
erk Hess
U
se
SIMD bonde
d
s
w
i
thout pertu
r
bed interactions
commit
|
commitdiff
|
tree
2018-02-08
B
erk
Hess
Allow bonds with
distanc
e
=0
commit
|
commitdiff
|
tree
2018-02-05
B
e
rk Hess
S
e
t cutoff modifiers in forcerec
commit
|
commitdiff
|
tree
2018-02-05
Berk Hess
F
i
x assertion fail
u
re
in TPI
commit
|
commitdiff
|
tree
2018-01-30
Berk Hess
Remove
d
u
n
us
e
d flag PCA_CAN_READ_NODE
commit
|
commitdiff
|
tree
2018-01-18
Berk Hess
Fix
C
OMM removal on part of
t
he system
commit
|
commitdiff
|
tree
2018-01-18
Berk Hess
Add check in
g
rompp to avoid assertion fa
i
l
ure
commit
|
commitdiff
|
tree
2018-01-17
B
e
rk Hess
Repla
c
e stder
r
prints in f
i
lenm
.
cpp by assert
s
commit
|
commitdiff
|
tree
2018-01-17
Berk He
s
s
Re-e
n
able GPU
w
it
h
w
alls an
d
1 energy group
commit
|
commitdiff
|
tree
2018-01-16
Berk Hess
Rem
o
ve t
u
mbling ic
e
-cu
b
e
w
a
rning wit
h
SD
commit
|
commitdiff
|
tree
2018-01-16
Ber
k
Hess
A
v
o
id
m
drun echoing "No optio
n
-mu
l
ti"
commit
|
commitdiff
|
tree
2018-01-09
Berk
H
ess
Rewo
r
d
C
PU/GPU i
m
balance
n
otes
commit
|
commitdiff
|
tree
2018-01-09
Berk Hess
Do not turn on DLB
a
t
r
e
p
li
c
a exchange
commit
|
commitdiff
|
tree
2018-01-08
Berk Hess
F
i
x t
r
iclinic domain decomp
o
sit
i
on bug
commit
|
commitdiff
|
tree
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