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Set buffers appropriately so .xpm files can be read.
2020-02-27
Pascal Mer
z
Lo
o
s
e
n gm
x
api stop
s
ig
n
a
ler test
commit
|
commitdiff
|
tree
2020-02-27
Pas
c
al M
e
rz
Use
legacy code path for t_graph
(mod
u
lar simulator)
commit
|
commitdiff
|
tree
2020-02-27
Pascal Merz
Extract and
expose fu
n
ction
t
o dete
r
m
i
ne whether molecules
.
.
.
commit
|
commitdiff
|
tree
2020-02-26
Pascal
M
e
r
z
Fix c
o
nst
r
aint contribution
t
o dhdl (mo
d
ular s
i
m
u
l
ator)
commit
|
commitdiff
|
tree
2020-02-26
Pasc
a
l Merz
Fix c
a
lculation of r
e
ci
p
r
o
cal te
r
ms in rerun
commit
|
commitdiff
|
tree
2020-02-21
Pa
s
cal Merz
Us
e
legacy co
d
e
p
ath
f
or
N
MR
restrai
n
ts (mo
d
ular si
m
ula
t
or)
commit
|
commitdiff
|
tree
2020-02-21
P
ascal Me
r
z
Corr
e
ct for
s
k
ewe
d
box
in non-DD modular simulator
commit
|
commitdiff
|
tree
2020-02-14
P
ascal Merz
Expand
t
est cover
a
g
e of
exact continua
t
ion tests
commit
|
commitdiff
|
tree
2020-02-14
Pascal M
e
rz
Fix re
a
din
g
of checkpoints with
P
arrine
l
l
o
-Rahm
a
n
.
.
.
commit
|
commitdiff
|
tree
2020-02-14
P
ascal Merz
Fix Parrine
l
l
o-Rahman s
c
a
l
i
n
g on initial step (modular
.
.
.
commit
|
commitdiff
|
tree
2020-02-14
Pasca
l
Merz
Move m
o
dular simulator
d
ecisio
n
before checkpoint loading
commit
|
commitdiff
|
tree
2020-02-13
Pascal
Me
r
z
Fix checkNumberOfB
o
n
dedInt
e
ract
i
ons
b
ug
commit
|
commitdiff
|
tree
2020-02-13
Pascal Merz
E
x
pose vsite counting
commit
|
commitdiff
|
tree
2019-12-17
Pasc
a
l Merz
F
i
x
e
xact continu
a
tion m
o
dular simulator
commit
|
commitdiff
|
tree
2019-12-12
P
a
s
cal Merz
Test
f
or ex
p
ected output
files
commit
|
commitdiff
|
tree
2019-12-12
Pasca
l
Merz
Fix final configuration writ
i
ng
f
or modular simu
l
ator
commit
|
commitdiff
|
tree
2019-10-31
P
asc
a
l M
e
rz
C
h
eck for contrad
i
c
ting
e
nviron
m
e
nt var
i
ables (modular
.
.
.
commit
|
commitdiff
|
tree
2019-10-30
Pasc
a
l Merz
Fix doxyge
n
for modular
s
imula
t
or
commit
|
commitdiff
|
tree
2019-10-30
Pascal M
e
rz
Fix m
o
dular simulator
d
o
c
umentation
commit
|
commitdiff
|
tree
2019-10-29
Pasc
a
l Merz
Fix co
m
pa
t
ibility
c
heck of m
o
dula
r
simulator
commit
|
commitdiff
|
tree
2019-10-27
Pascal Merz
Enable forc
e
d rotatio
n
for modular simula
t
or
commit
|
commitdiff
|
tree
2019-10-23
P
ascal Merz
C
orrect for skewed box before domain d
e
composition
.
.
.
commit
|
commitdiff
|
tree
2019-10-23
Pascal Merz
Fix
l
og writing (modular s
i
mulator)
commit
|
commitdiff
|
tree
2019-10-23
Pas
c
a
l
M
erz
A
d
apt enu
m
to style
c
o
n
vention (modular s
i
mulator)
commit
|
commitdiff
|
tree
2019-10-23
Pasca
l
M
erz
S
mall improveme
n
t t
o
Energ
y
Element (modular simu
l
ator)
commit
|
commitdiff
|
tree
2019-10-22
Pascal
Merz
Fi
x
st
o
p
condition h
a
ndlin
g
(modular s
i
mula
t
o
r
)
commit
|
commitdiff
|
tree
2019-10-22
P
ascal Merz
Fix si
g
nal propa
g
ation (modu
l
a
r simulator)
commit
|
commitdiff
|
tree
2019-10-22
P
a
scal
Merz
F
i
x Dom
D
ec step (mo
d
u
l
a
r
simulator)
commit
|
commitdiff
|
tree
2019-10-22
Pascal
Merz
F
ix PmeLoadBalanceHelper in
i
tialization (mod
u
l
a
r simul
a
tor)
commit
|
commitdiff
|
tree
2019-10-01
Pasc
a
l Merz
Output corr
e
ct kinetic at last
step (modular simulator
)
commit
|
commitdiff
|
tree
2019-09-23
Pascal
M
e
r
z
Parrinello-Ra
h
man
f
o
r md-vv
commit
|
commitdiff
|
tree
2019-09-23
Pas
c
al Merz
Parrinello-Rahman
barosta
t
f
o
r m
o
dular
s
imulator (leap
.
.
.
commit
|
commitdiff
|
tree
2019-09-23
Pa
s
cal Merz
Zero pressure an
d
viria
l
tensors at
beginning of step
commit
|
commitdiff
|
tree
2019-09-23
Pas
c
a
l Me
r
z
Intr
o
du
c
e FEP int
o
modul
a
r
s
im
u
lator
commit
|
commitdiff
|
tree
2019-09-23
Pascal M
e
rz
Make CheckpointHelper safer a
n
d easier to
u
se
commit
|
commitdiff
|
tree
2019-09-23
Pasc
a
l
Merz
Fix
vrescale t
h
e
rmostat in
t
egral
(
m
odul
a
r
simulator)
commit
|
commitdiff
|
tree
2019-09-20
Pascal Merz
F
ix restarts in modular si
m
ula
t
o
r
commit
|
commitdiff
|
tree
2019-09-20
Pascal Merz
Fix domdec for md-vv modu
l
ar s
i
mulator
commit
|
commitdiff
|
tree
2019-09-20
Pascal Merz
Ru
n
s
imul
a
tor equiv
a
lence tests in do
u
ble prec
i
si
o
n
.
.
.
commit
|
commitdiff
|
tree
2019-09-18
Pas
c
al Merz
v-rescale thermostat for
m
odular simul
a
tor
commit
|
commitdiff
|
tree
2019-09-17
Pasca
l
Merz
M
i
n
or
tweaks to sum_d
h
dl and
setCurrentLambd
a
s
L
ocal
commit
|
commitdiff
|
tree
2019-09-17
Pascal Merz
F
ix position pi
n
ning for modul
a
r sim
u
lator
commit
|
commitdiff
|
tree
2019-09-17
Pascal Merz
Fix modu
l
ar s
i
mulato
r
MPI bugs
commit
|
commitdiff
|
tree
2019-09-17
Pa
s
cal Merz
M
a
ke modular simulato
r
the
d
efau
l
t code path for
m
d
.
.
.
commit
|
commitdiff
|
tree
2019-09-17
Pascal Merz
F
i
x
force eleme
n
t
commit
|
commitdiff
|
tree
2019-09-17
Pascal Merz
Ena
b
le chec
k
pointing for modular simula
t
or
commit
|
commitdiff
|
tree
2019-09-15
Pascal Merz
Introduce the modular simulator
commit
|
commitdiff
|
tree
2019-09-12
Pas
c
al Merz
Upd
a
t
e
modular simulator
tes
t
s
commit
|
commitdiff
|
tree
2019-09-10
Pascal Merz
Composit
e
SimulatorElement
f
o
r
t
he modular simu
l
ator
commit
|
commitdiff
|
tree
2019-09-10
Pascal Merz
C
o
ordinate Propa
g
ators
commit
|
commitdiff
|
tree
2019-09-10
Pascal Merz
State
P
ropag
a
torData:
I
n
t
r
odu
c
ed cons
t
box ac
c
essor
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
P
a
scal M
e
rz
Add trivi
a
l
const
q
u
a
lifiers to shel
l
fc a
n
d EnergyOutput
commit
|
commitdiff
|
tree
2019-09-10
Pascal
M
e
r
z
Co
n
straint element for the mod
u
lar simulator
commit
|
commitdiff
|
tree
2019-09-09
Pasc
a
l Merz
D
omain decompositio
n
and PME load balancing for modular
.
.
.
commit
|
commitdiff
|
tree
2019-09-07
P
a
scal Me
r
z
Make pme_loadbal_do() independent of
t_sta
t
e
commit
|
commitdiff
|
tree
2019-09-07
P
a
scal Merz
Forc
e
Ele
m
ent and ShellFCE
l
e
m
ent for the modular simulator
commit
|
commitdiff
|
tree
2019-09-06
P
as
c
al Merz
ComputeGlobalsE
l
ement for the modula
r
simulator
commit
|
commitdiff
|
tree
2019-09-05
P
a
scal
Me
r
z
Introduce
topol
o
gy class
f
or mod
u
l
ar simulator
commit
|
commitdiff
|
tree
2019-09-05
Pascal Merz
Rename MicroState
to StatePropagatorData f
o
r modular
.
.
.
commit
|
commitdiff
|
tree
2019-09-05
Pascal Merz
Ada
p
t inh
e
ri
t
ance inte
n
dati
o
n to u
n
crustif
y
commit
|
commitdiff
|
tree
2019-09-05
Pascal Merz
M
ake
d
o_
c
onstrain_first() independent of t_s
t
at
e
commit
|
commitdiff
|
tree
2019-09-03
Pascal Merz
Introduce
e
nerg
y
el
e
ment for modular
s
imulator
commit
|
commitdiff
|
tree
2019-08-28
Pascal M
e
rz
Introduc
e
M
i
croState for modular
s
i
mulator
commit
|
commitdiff
|
tree
2019-08-28
Pascal Merz
I
ntroduce signallers for
modular integrator
commit
|
commitdiff
|
tree
2019-08-28
P
asc
a
l Mer
z
Introduc
e
t
he ma
i
n
m
od
u
lar
s
imulator
inte
r
faces and
.
.
.
commit
|
commitdiff
|
tree
2019-08-12
Pascal Merz
U
se new
s
e
t
en
v
function for ene
r
gyoutp
u
t t
e
st
commit
|
commitdiff
|
tree
2019-08-05
Pascal Merz
Add
tri
v
ia
l
const
q
uali
f
ier to energ
y
o
u
tput
commit
|
commitdiff
|
tree
2019-08-05
P
ascal Mer
z
A
dd
co
n
s
t gette
r
t
o MDAto
m
s
commit
|
commitdiff
|
tree
2019-08-05
Pasca
l
Merz
Mo
v
e owners
h
ip o
f
kinetic
e
nergy
object t
o
ISim
u
l
ator
commit
|
commitdiff
|
tree
2019-08-05
Pascal Me
r
z
Added Simulator comp
a
rison
test
commit
|
commitdiff
|
tree
2019-08-05
Pascal Merz
Introduce S
i
m
ulatorBuilder
commit
|
commitdiff
|
tree
2019-08-02
Pasc
a
l Merz
Introduce Simulator
b
ase cla
s
s
commit
|
commitdiff
|
tree
2019-07-31
Pasca
l
M
e
rz
Rename Sim
u
l
ator to Le
g
acySimul
a
tor
commit
|
commitdiff
|
tree
2019-07-11
Pascal Merz
G
et rid of clang-tidy
w
arning
i
n do_
m
d/rerun/
m
imic
commit
|
commitdiff
|
tree
2019-07-11
Pas
c
al Merz
Rem
o
ve depe
n
de
n
ce of compu
t
e_
g
lobal
s
o
n t_state
commit
|
commitdiff
|
tree
2019-07-11
Pascal Merz
Mak
e
relax_shell_flexcon
i
ndepende
n
t
o
f
t_stat
e
commit
|
commitdiff
|
tree
2019-07-09
Pascal
M
erz
A
dded trivial
const qualif
i
er to relax_s
h
ell_fl
e
x
con()
commit
|
commitdiff
|
tree
2019-07-09
Pascal
Mer
z
Const qualifier for forces in update_c
o
ords
commit
|
commitdiff
|
tree
2019-07-01
Pas
c
al Merz
Fi
x
module detection for physical v
a
li
d
ation
commit
|
commitdiff
|
tree
2019-06-24
Pascal Merz
Make
global to
p
ology
con
s
tant in
trajectory wri
t
ing
commit
|
commitdiff
|
tree
2019-05-27
Pas
c
al Merz
Clean
u
p
renamed simulator
.
h file
commit
|
commitdiff
|
tree
2019-05-25
Pascal Merz
Remove dependence of mdoutf_write_to
_
trajectory_files
.
.
.
commit
|
commitdiff
|
tree
2019-05-25
Pas
c
al Me
r
z
R
ename
I
ntegrator
class
commit
|
commitdiff
|
tree
2019-05-16
Pascal Mer
z
Use Pyt
h
o
n 3
commit
|
commitdiff
|
tree
2018-12-10
Pascal Merz
Failp
r
oof signal conversion
commit
|
commitdiff
|
tree
2018-09-26
Pascal Merz
(Re-)fix typo
i
n DD load
balanc
i
n
g pri
n
ting
commit
|
commitdiff
|
tree
2018-09-25
Pasc
a
l Merz
Remove obsolete braces in
do_m
d
(
)
commit
|
commitdiff
|
tree
2018-09-25
Pascal
Me
r
z
Remove rerun from
d
o_md
commit
|
commitdiff
|
tree
2018-09-25
P
ascal Merz
Remo
v
e u
n
nec
e
ss
a
r
y
f
unctionality from d
o
_rerun
commit
|
commitdiff
|
tree
2018-09-25
Pascal M
e
rz
Prepare rerun commit
commit
|
commitdiff
|
tree
2018-09-21
Pascal
Merz
Make CG
L
O
_CHECK_N
U
MBER_
O
F
_
BONDE
D
_
I
NTERACTIONS requi
r
e
.
.
.
commit
|
commitdiff
|
tree
2018-09-18
Pascal
Merz
Do
c
um
e
n
t
ation
fix: Rerun an
d
nstlist
commit
|
commitdiff
|
tree
2018-09-18
Pascal Merz
Int
r
oduce stop handler
commit
|
commitdiff
|
tree
2018-09-18
Pascal Mer
z
I
ntroduce checkpo
i
nt handler
commit
|
commitdiff
|
tree
2018-09-18
Pa
s
cal Merz
Intr
o
d
uc
e
r
eset han
d
l
e
r
commit
|
commitdiff
|
tree
2018-09-17
Pasc
a
l
Merz
Fix
t
y
po in DD
load balancing printing
commit
|
commitdiff
|
tree
2018-09-11
Pascal Merz
Adde
d
trivial c
o
nst qu
a
lifiers
commit
|
commitdiff
|
tree
2018-09-11
P
a
sca
l
Merz
Initialize total_vir and
p
res in init_m
d
commit
|
commitdiff
|
tree
2018-04-04
Pasc
a
l M
e
rz
Move check
N
u
m
berOfBondedIn
t
eractions
commit
|
commitdiff
|
tree
2017-12-21
Pasc
a
l Merz
Do
c
umen
t
a
t
i
on a
n
d fi
x
es fo
r
p
hysical val
i
dation
commit
|
commitdiff
|
tree
next