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GROMACS 2020 release candidate
2019-12-17
Pascal Merz
F
ix exact continuati
o
n modu
l
ar simulator
commit
|
commitdiff
|
tree
2019-12-12
Pascal Merz
Test
for
e
xpected o
u
tput
f
iles
commit
|
commitdiff
|
tree
2019-12-12
Pas
c
al
Merz
Fi
x
final con
f
iguration w
r
iting for
m
o
dular
s
imulator
commit
|
commitdiff
|
tree
2019-10-31
Pascal Merz
Chec
k
for contradicting
e
nvi
r
o
n
ment
v
ariables
(
m
o
dular
.
.
.
commit
|
commitdiff
|
tree
2019-10-30
Pascal Me
r
z
Fix doxygen for modular simulator
commit
|
commitdiff
|
tree
2019-10-30
Pascal Merz
Fix modu
l
ar simul
a
tor documentation
commit
|
commitdiff
|
tree
2019-10-29
Pascal Me
r
z
F
ix
c
ompatibility check
o
f
m
odular sim
u
lator
commit
|
commitdiff
|
tree
2019-10-27
P
ascal Merz
Enable forced rotation
for modul
a
r simul
a
t
or
commit
|
commitdiff
|
tree
2019-10-23
Pascal Merz
Correct
f
or skewed
b
ox before domain
decomposition
.
.
.
commit
|
commitdiff
|
tree
2019-10-23
Pa
s
cal Mer
z
Fix log writing (
m
odul
a
r s
i
mulator)
commit
|
commitdiff
|
tree
2019-10-23
Pascal Merz
Adap
t
enum t
o
style
c
onventi
o
n (modula
r
simula
t
or)
commit
|
commitdiff
|
tree
2019-10-23
Pascal Merz
Sma
l
l improvem
e
nt to EnergyElement (
m
odu
l
a
r simulator)
commit
|
commitdiff
|
tree
2019-10-22
Pascal M
e
rz
Fix stop
c
ondition handling (modular simulator)
commit
|
commitdiff
|
tree
2019-10-22
Pascal Merz
Fix si
g
nal propa
g
ation (modular
simulator)
commit
|
commitdiff
|
tree
2019-10-22
Pascal Merz
F
ix DomDec step (modu
l
ar si
m
u
lator)
commit
|
commitdiff
|
tree
2019-10-22
Pascal Mer
z
Fix
PmeLoadBal
a
nceHelp
e
r
initial
i
zation (modular si
m
ulator)
commit
|
commitdiff
|
tree
2019-10-01
Pascal Merz
Out
p
ut correct
ki
n
etic at last step (modu
l
ar
s
imul
a
tor)
commit
|
commitdiff
|
tree
2019-09-23
Pascal Merz
Parri
n
ell
o
-Rahman for
m
d
-vv
commit
|
commitdiff
|
tree
2019-09-23
Pasc
a
l
M
erz
Parrinello-Rahman barostat for modul
a
r simulator (leap
.
.
.
commit
|
commitdiff
|
tree
2019-09-23
Pascal Merz
Zero
pr
e
ssure
a
nd viria
l
tensors at beginnin
g
of step
commit
|
commitdiff
|
tree
2019-09-23
Pas
c
al Merz
Introduce F
E
P into m
o
dular simul
a
t
o
r
commit
|
commitdiff
|
tree
2019-09-23
Pasca
l
Merz
M
a
ke C
h
eckpointHelper safer and easier
t
o use
commit
|
commitdiff
|
tree
2019-09-23
Pascal Merz
Fix
vrescale
t
he
r
mostat integral (modular
s
im
u
la
t
o
r
)
commit
|
commitdiff
|
tree
2019-09-20
Pascal M
e
rz
Fix restarts in modular simulator
commit
|
commitdiff
|
tree
2019-09-20
Pa
s
cal
M
er
z
Fix
d
o
md
e
c
f
or
m
d-vv modula
r
simulator
commit
|
commitdiff
|
tree
2019-09-20
Pascal Merz
R
un simulator equival
e
nce tests in dou
b
le p
r
ecision
.
.
.
commit
|
commitdiff
|
tree
2019-09-18
Pa
s
cal Merz
v-rescale ther
m
osta
t
for modul
a
r
simulato
r
commit
|
commitdiff
|
tree
2019-09-17
P
a
scal M
e
rz
Mino
r
tweaks
t
o sum_dhdl and setCurrentLa
m
bdasLocal
commit
|
commitdiff
|
tree
2019-09-17
Pascal Merz
Fi
x
position pinning for m
o
dular simulator
commit
|
commitdiff
|
tree
2019-09-17
Pascal
M
erz
Fix mo
d
ular
si
m
ulator MPI bugs
commit
|
commitdiff
|
tree
2019-09-17
Pascal M
e
r
z
Ma
k
e modul
a
r simulator the default
c
ode path for md
.
.
.
commit
|
commitdiff
|
tree
2019-09-17
Pascal
M
erz
Fix fo
r
ce element
commit
|
commitdiff
|
tree
2019-09-17
Pascal
M
e
rz
Enab
l
e checkpointi
n
g
f
or
modul
a
r
simulator
commit
|
commitdiff
|
tree
2019-09-15
Pasc
a
l M
e
r
z
I
n
trod
u
ce the modular sim
u
l
a
tor
commit
|
commitdiff
|
tree
2019-09-12
P
a
scal Merz
Update mo
d
ular si
m
u
l
ato
r
t
e
s
ts
commit
|
commitdiff
|
tree
2019-09-10
P
ascal Merz
CompositeSimul
a
tor
E
lem
e
nt for the modular s
i
m
u
lato
r
commit
|
commitdiff
|
tree
2019-09-10
Pascal M
e
r
z
Coordinate Pr
o
pagato
r
s
commit
|
commitdiff
|
tree
2019-09-10
Pas
c
al Merz
StatePropagatorData: Introduced
const box ac
c
essor
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Pascal Merz
Ad
d
trivial const qualifiers t
o
shellfc a
n
d EnergyOut
p
ut
commit
|
commitdiff
|
tree
2019-09-10
Pascal
M
e
r
z
Co
n
st
r
ain
t
element for the mod
u
lar simulator
commit
|
commitdiff
|
tree
2019-09-09
Pascal M
e
rz
D
o
main decomposition an
d
PME load balan
c
ing for modular
.
.
.
commit
|
commitdiff
|
tree
2019-09-07
Pascal Merz
M
a
ke
pme_
l
oadbal_do() in
d
epe
n
dent o
f
t_state
commit
|
commitdiff
|
tree
2019-09-07
P
ascal Merz
ForceE
l
e
m
ent and ShellFCElement for t
h
e modu
l
ar s
i
mulator
commit
|
commitdiff
|
tree
2019-09-06
Pascal Merz
ComputeGlo
b
alsEleme
n
t for the modular simulator
commit
|
commitdiff
|
tree
2019-09-05
Pasc
a
l
Merz
Introduce topology class for mo
d
ular simulator
commit
|
commitdiff
|
tree
2019-09-05
Pascal Merz
Rename MicroStat
e
to StatePropaga
t
or
D
ata for modula
r
.
.
.
commit
|
commitdiff
|
tree
2019-09-05
Pa
s
c
a
l Merz
Adapt
i
n
heritanc
e
intend
a
tion to unc
r
ustify
commit
|
commitdiff
|
tree
2019-09-05
Pascal Merz
M
a
ke do_constrain_first() independent of t_stat
e
commit
|
commitdiff
|
tree
2019-09-03
Pa
s
cal M
e
rz
Introduce energy el
e
ment f
o
r mod
u
lar simulator
commit
|
commitdiff
|
tree
2019-08-28
Pas
c
al M
e
rz
Intro
d
uce MicroState f
o
r modular
s
i
mul
a
tor
commit
|
commitdiff
|
tree
2019-08-28
Pascal Merz
Intro
d
u
c
e
s
i
gnallers for modular
int
e
grator
commit
|
commitdiff
|
tree
2019-08-28
Pasc
a
l Mer
z
I
ntrodu
c
e the main modular simulat
o
r interfa
c
es and
.
.
.
commit
|
commitdiff
|
tree
2019-08-12
Pasca
l
Me
r
z
Use new s
e
t
env
function for energ
y
o
utp
u
t t
e
st
commit
|
commitdiff
|
tree
2019-08-05
Pasc
a
l Merz
Add trivial const qualifier to e
n
e
r
gy out
p
ut
commit
|
commitdiff
|
tree
2019-08-05
Pascal Merz
Add co
n
s
t
get
t
er t
o
MDA
t
oms
commit
|
commitdiff
|
tree
2019-08-05
Pascal Mer
z
M
ove ownership of ki
n
etic energy o
b
ject to ISimu
l
ator
commit
|
commitdiff
|
tree
2019-08-05
Pascal M
e
rz
A
d
ded Simulator comparison test
commit
|
commitdiff
|
tree
2019-08-05
P
a
s
c
al Merz
Introdu
c
e
Si
m
u
latorBuilder
commit
|
commitdiff
|
tree
2019-08-02
Pascal Merz
In
t
roduce S
i
mulator
base class
commit
|
commitdiff
|
tree
2019-07-31
P
a
s
c
a
l
Merz
Rena
m
e Simulator to Legacy
S
imul
a
tor
commit
|
commitdiff
|
tree
2019-07-11
P
a
scal Merz
Get
rid of cl
a
ng-
t
idy w
a
rning in
d
o_md/rerun/mi
m
i
c
commit
|
commitdiff
|
tree
2019-07-11
Pasca
l
Mer
z
Remo
v
e dependence of compute
_
glob
a
ls
on t_state
commit
|
commitdiff
|
tree
2019-07-11
Pascal Merz
M
ake
r
elax
_
shell_
f
lexc
o
n independent of t_state
commit
|
commitdiff
|
tree
2019-07-09
Pasca
l
Mer
z
Added t
r
ivi
a
l const
q
ualifie
r
to relax_she
l
l_flexcon
(
)
commit
|
commitdiff
|
tree
2019-07-09
Pascal Merz
C
onst qua
l
ifier f
o
r for
c
es in u
p
dat
e
_c
o
ords
commit
|
commitdiff
|
tree
2019-07-01
Pas
c
al
M
e
rz
F
ix module detection f
o
r
physical validat
i
o
n
commit
|
commitdiff
|
tree
2019-06-24
Pa
s
cal Mer
z
M
ake gl
o
bal topology constant
in tr
a
j
e
c
tory writing
commit
|
commitdiff
|
tree
2019-05-27
Pascal Merz
Clean
up renamed simulator
.
h file
commit
|
commitdiff
|
tree
2019-05-25
Pascal Merz
R
emove
d
ependence of mdout
f
_write_to_tr
a
jectory_files
.
.
.
commit
|
commitdiff
|
tree
2019-05-25
Pascal Merz
Re
n
am
e
Integr
a
t
or class
commit
|
commitdiff
|
tree
2019-05-16
Pascal Merz
Us
e
Python 3
commit
|
commitdiff
|
tree
2018-12-10
Pascal Me
r
z
Failp
r
o
o
f
s
i
g
nal con
v
ersion
commit
|
commitdiff
|
tree
2018-09-26
Pascal Merz
(Re-)fix typ
o
i
n
DD load
b
alancing printing
commit
|
commitdiff
|
tree
2018-09-25
Pascal Merz
Remove obsolete braces in do_md
(
)
commit
|
commitdiff
|
tree
2018-09-25
Pascal Mer
z
Rem
o
ve
r
er
u
n from do_md
commit
|
commitdiff
|
tree
2018-09-25
Pasc
a
l Merz
Remove un
n
e
cessary functionality from
do_rerun
commit
|
commitdiff
|
tree
2018-09-25
Pasc
a
l
M
erz
Prepar
e
re
r
un comm
i
t
commit
|
commitdiff
|
tree
2018-09-21
Pascal Merz
Make CGLO_CHECK_
N
UMBER_
O
F_BOND
E
D_
I
NTERAC
T
IONS require
.
.
.
commit
|
commitdiff
|
tree
2018-09-18
Pasc
a
l Merz
Do
c
ument
a
tion fix: Rerun and
nstlist
commit
|
commitdiff
|
tree
2018-09-18
P
ascal Merz
Introduce stop handler
commit
|
commitdiff
|
tree
2018-09-18
Pascal Merz
Introduce
c
heckpoint handler
commit
|
commitdiff
|
tree
2018-09-18
P
a
sc
a
l Merz
Introduce reset
handler
commit
|
commitdiff
|
tree
2018-09-17
Pascal Merz
Fix typo i
n
D
D
load
b
a
lancing p
r
i
n
tin
g
commit
|
commitdiff
|
tree
2018-09-11
Pascal M
e
rz
Added trivial
c
onst
q
ualifiers
commit
|
commitdiff
|
tree
2018-09-11
Pas
c
al M
e
r
z
Initialize total_vir and pres in init_md
commit
|
commitdiff
|
tree
2018-04-04
P
a
s
cal Merz
Move checkNumberOfBonded
I
n
t
e
r
actions
commit
|
commitdiff
|
tree
2017-12-21
Pascal M
e
rz
Documentation and fixes for physical
validati
o
n
commit
|
commitdiff
|
tree
2017-11-22
Pas
c
al
Merz
Pr
o
o
f of co
n
cept:
P
h
y
s
i
cal validatio
n
suite
commit
|
commitdiff
|
tree