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Fix gmx h2order -d option
2020-11-10
Pa
s
cal
Merz
Fix MTTK constant energy bugs
commit
|
commitdiff
|
tree
2020-09-30
Pascal
M
e
rz
Fix bug
rese
t
tin
g
mdatoms mas
s
es to la
m
bda
=
0
state
commit
|
commitdiff
|
tree
2020-04-14
Pascal M
e
rz
Rei
n
t
roduce LJ
E
wald tables
commit
|
commitdiff
|
tree
2020-04-03
Pascal Merz
F
i
x expanded ensem
b
l
e
on check
p
oint
r
estarts
commit
|
commitdiff
|
tree
2020-02-27
Pascal M
e
rz
Loosen gmxapi stop
s
ignale
r
test
commit
|
commitdiff
|
tree
2020-02-27
P
ascal Merz
Use
l
e
gacy
code path for t_gra
p
h (modular s
i
mul
a
tor)
commit
|
commitdiff
|
tree
2020-02-27
Pasca
l
Mer
z
Extract
a
nd expose
f
unction to dete
r
min
e
whether molecu
l
es
.
.
.
commit
|
commitdiff
|
tree
2020-02-26
P
a
s
c
al Merz
Fix cons
t
rai
n
t co
n
tri
b
utio
n
to
dhdl (modula
r
si
m
ulat
o
r
)
commit
|
commitdiff
|
tree
2020-02-26
Pascal Merz
F
ix calcula
t
ion of reci
p
roc
a
l terms in
r
e
run
commit
|
commitdiff
|
tree
2020-02-21
Pascal Merz
Use
legacy code
p
ath for NMR res
t
ra
i
nts (modular
simulator)
commit
|
commitdiff
|
tree
2020-02-21
Pascal Merz
Correct
f
or sk
e
wed
b
o
x
in
n
on-DD modula
r
si
m
ulator
commit
|
commitdiff
|
tree
2020-02-14
Pascal Merz
Exp
a
nd
test coverag
e
o
f
exa
c
t
co
n
t
i
n
ua
t
ion t
e
sts
commit
|
commitdiff
|
tree
2020-02-14
Pascal M
e
rz
Fix re
a
di
n
g
of
c
hec
k
p
o
ints
w
i
t
h P
a
rrinello-Rahman
.
.
.
commit
|
commitdiff
|
tree
2020-02-14
Pasca
l
Merz
Fix Parrinell
o
-Rahman scal
i
ng on in
i
tial step
(
modular
.
.
.
commit
|
commitdiff
|
tree
2020-02-14
Pas
c
a
l
Me
r
z
Move modu
l
ar simu
l
a
t
or deci
s
ion before ch
e
ckpoint
l
oad
i
ng
commit
|
commitdiff
|
tree
2020-02-13
Pascal Merz
F
ix checkNu
m
berOf
B
onde
d
Interactions bug
commit
|
commitdiff
|
tree
2020-02-13
Pascal Merz
Expose
v
s
ite counting
commit
|
commitdiff
|
tree
2019-12-17
Pascal
M
er
z
Fix e
x
act c
o
ntinuation modular simulator
commit
|
commitdiff
|
tree
2019-12-12
Pa
s
ca
l
Mer
z
Test
f
or expect
e
d outp
u
t
fi
l
e
s
commit
|
commitdiff
|
tree
2019-12-12
P
asca
l
Mer
z
Fix final config
u
ration writ
i
ng for mod
u
lar simulator
commit
|
commitdiff
|
tree
2019-10-31
Pascal
M
erz
Check for
c
ontradictin
g
environ
m
en
t
v
a
r
i
ables (modul
a
r
.
.
.
commit
|
commitdiff
|
tree
2019-10-30
P
a
scal Mer
z
Fix doxygen for modular simulator
commit
|
commitdiff
|
tree
2019-10-30
Pasca
l
Me
r
z
Fix modular simula
t
or documentation
commit
|
commitdiff
|
tree
2019-10-29
P
as
c
al Me
r
z
Fix compati
b
ility check of
m
odu
l
ar simula
t
or
commit
|
commitdiff
|
tree
2019-10-27
Pascal M
e
rz
Enab
l
e forced r
o
t
a
tio
n
for
m
odular si
m
ulator
commit
|
commitdiff
|
tree
2019-10-23
Pascal M
e
r
z
Correct for s
k
ewed box before domai
n
d
e
compo
s
ition
.
.
.
commit
|
commitdiff
|
tree
2019-10-23
Pascal Merz
F
ix log wr
i
ti
n
g (
m
odular simulator
)
commit
|
commitdiff
|
tree
2019-10-23
Pascal Merz
Adap
t
enum
to style
convention (modu
l
a
r
simulator)
commit
|
commitdiff
|
tree
2019-10-23
Pa
s
c
a
l M
e
rz
Small i
m
provement
t
o En
e
rg
y
E
l
e
ment (m
o
d
u
lar simu
l
ator)
commit
|
commitdiff
|
tree
2019-10-22
P
ascal Merz
Fix
stop condition ha
n
dlin
g
(
m
odu
l
ar
simulator)
commit
|
commitdiff
|
tree
2019-10-22
Pas
c
al Merz
Fix signa
l
propagation (m
o
dular simulat
o
r)
commit
|
commitdiff
|
tree
2019-10-22
P
ascal Me
r
z
Fix
D
o
mDec step
(
modular
simulator)
commit
|
commitdiff
|
tree
2019-10-22
Pascal Merz
Fix PmeLoadBalanceH
e
lper i
n
itial
i
zation (modular simulator)
commit
|
commitdiff
|
tree
2019-10-01
Pas
c
a
l
Mer
z
Output corre
c
t
ki
n
et
i
c a
t
las
t
s
t
e
p
(modular sim
u
lator)
commit
|
commitdiff
|
tree
2019-09-23
Pascal Merz
Parri
n
ello-Rahman f
o
r md-vv
commit
|
commitdiff
|
tree
2019-09-23
P
ascal Merz
Parrinello-Rahman barostat for mo
d
ula
r
simul
a
t
or
(leap
.
.
.
commit
|
commitdiff
|
tree
2019-09-23
Pascal M
e
rz
Zero pressure a
n
d vir
i
al tensors at begin
n
ing o
f
step
commit
|
commitdiff
|
tree
2019-09-23
Pascal Merz
In
t
ro
d
uce FEP into mo
d
ular s
i
mula
t
or
commit
|
commitdiff
|
tree
2019-09-23
Pascal Merz
Make CheckpointHe
l
per safer and easier to use
commit
|
commitdiff
|
tree
2019-09-23
Pascal Me
r
z
Fix v
r
escale
t
h
e
rmostat integr
a
l (mod
u
l
a
r simul
a
tor)
commit
|
commitdiff
|
tree
2019-09-20
Pasc
a
l M
e
rz
Fix restarts in modul
a
r
simulat
o
r
commit
|
commitdiff
|
tree
2019-09-20
Pascal Merz
Fix
d
o
m
d
ec for
m
d-vv m
o
dular
s
imulat
o
r
commit
|
commitdiff
|
tree
2019-09-20
Pas
c
al M
e
r
z
Ru
n
s
imu
l
a
tor equivalence t
e
sts i
n
dou
b
le precision
.
.
.
commit
|
commitdiff
|
tree
2019-09-18
Pascal
M
e
rz
v-resca
l
e thermostat for modular s
i
mulator
commit
|
commitdiff
|
tree
2019-09-17
P
ascal Merz
Minor twea
k
s to sum_dhd
l
and setCur
r
en
t
La
m
bdasL
o
cal
commit
|
commitdiff
|
tree
2019-09-17
P
a
s
c
al M
e
r
z
Fix pos
i
tion pinn
i
ng for modul
a
r s
i
m
u
l
ator
commit
|
commitdiff
|
tree
2019-09-17
Pascal Merz
Fix modular simulator MPI bugs
commit
|
commitdiff
|
tree
2019-09-17
Pas
c
a
l
Me
r
z
Make modular si
m
ulator the
d
efault c
o
de path for
md
.
.
.
commit
|
commitdiff
|
tree
2019-09-17
Pasc
a
l Merz
F
ix forc
e
el
e
ment
commit
|
commitdiff
|
tree
2019-09-17
Pascal Merz
E
n
a
ble checkpointi
n
g for
m
o
d
ular simulator
commit
|
commitdiff
|
tree
2019-09-15
Pa
s
ca
l
Merz
Introduce the
mod
u
lar si
m
ulator
commit
|
commitdiff
|
tree
2019-09-12
Pascal
Merz
Update m
o
dul
a
r simulat
o
r tests
commit
|
commitdiff
|
tree
2019-09-10
Pascal Merz
Composite
S
i
m
ulatorElement fo
r
the modul
a
r
simulator
commit
|
commitdiff
|
tree
2019-09-10
Pascal Merz
Coordin
a
t
e Propag
a
tors
commit
|
commitdiff
|
tree
2019-09-10
Pasca
l
Merz
Stat
e
Propagat
o
r
Data: Introduced c
o
nst box ac
c
e
s
s
or
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Pascal M
e
rz
A
dd trivi
a
l cons
t
q
u
ali
f
iers
t
o shellfc and E
n
ergyOutput
commit
|
commitdiff
|
tree
2019-09-10
Pascal
M
erz
Const
r
a
i
nt element for
the modular simulator
commit
|
commitdiff
|
tree
2019-09-09
Pascal M
e
rz
Dom
a
in decomposition
a
n
d PME load balanc
i
ng for modul
a
r
.
.
.
commit
|
commitdiff
|
tree
2019-09-07
Pascal Merz
Make pme_loa
d
bal_do() independent of t_state
commit
|
commitdiff
|
tree
2019-09-07
Pasc
a
l Merz
ForceElem
e
nt and ShellFCElemen
t
f
o
r
the modul
a
r simulator
commit
|
commitdiff
|
tree
2019-09-06
Pascal
M
erz
Co
m
puteGl
o
bal
s
E
l
em
e
nt
f
or the m
o
dular s
i
m
ulator
commit
|
commitdiff
|
tree
2019-09-05
Pascal Merz
In
t
r
odu
c
e
t
opology cl
a
ss for mo
d
ular simulat
o
r
commit
|
commitdiff
|
tree
2019-09-05
Pas
c
al Merz
Rename
M
i
c
roState to S
t
at
e
PropagatorDat
a
f
or
m
odular
.
.
.
commit
|
commitdiff
|
tree
2019-09-05
Pascal
M
e
r
z
Adap
t
inh
e
ritance inten
d
ation to un
c
rustify
commit
|
commitdiff
|
tree
2019-09-05
Pascal
Me
r
z
Make do_co
n
s
t
rai
n
_first() in
d
epen
d
ent of t_state
commit
|
commitdiff
|
tree
2019-09-03
Pa
s
cal Me
r
z
I
n
t
roduce energy element for modul
a
r
simulator
commit
|
commitdiff
|
tree
2019-08-28
Pascal Merz
Int
r
oduce M
i
croState for modular simu
l
ator
commit
|
commitdiff
|
tree
2019-08-28
Pasc
a
l M
e
rz
Introduce signa
l
lers for m
o
d
u
l
ar integrator
commit
|
commitdiff
|
tree
2019-08-28
Pascal Merz
Intro
d
uce the main modular simulator interfaces and
.
.
.
commit
|
commitdiff
|
tree
2019-08-12
Pascal Merz
Use ne
w
setenv f
u
ncti
o
n for
e
n
e
r
gyoutput test
commit
|
commitdiff
|
tree
2019-08-05
Pascal Merz
Add
trivial c
o
n
st qualifier to
e
n
ergy o
u
tput
commit
|
commitdiff
|
tree
2019-08-05
Pascal Merz
Add const getter to
M
DA
t
om
s
commit
|
commitdiff
|
tree
2019-08-05
P
a
s
cal Merz
Move o
w
n
e
r
s
h
i
p of
k
in
e
tic energy o
b
ject to I
S
imulat
o
r
commit
|
commitdiff
|
tree
2019-08-05
Pascal Merz
A
dd
e
d Si
m
ulat
o
r compa
r
is
o
n
tes
t
commit
|
commitdiff
|
tree
2019-08-05
Pasc
a
l Merz
Introduce
S
i
mulatorBuilder
commit
|
commitdiff
|
tree
2019-08-02
Pasc
a
l Merz
Introduce Simul
a
tor base class
commit
|
commitdiff
|
tree
2019-07-31
Pas
c
a
l
Merz
Rena
m
e Sim
u
lator to
L
e
gacySimulator
commit
|
commitdiff
|
tree
2019-07-11
Pascal Merz
Get rid
o
f clang-tidy warn
i
ng
in do_md
/
r
erun/mim
i
c
commit
|
commitdiff
|
tree
2019-07-11
Pascal
Merz
Remove depe
n
d
e
nce o
f
c
ompute_globals on t_state
commit
|
commitdiff
|
tree
2019-07-11
Pa
s
c
al
M
e
rz
Make relax_shell_flexcon independent
of t_state
commit
|
commitdiff
|
tree
2019-07-09
Pascal Merz
Added
t
rivial const
q
ualifi
e
r to relax_
s
hell_flexcon()
commit
|
commitdiff
|
tree
2019-07-09
Pas
c
al Merz
Co
n
st qua
l
if
i
er for forces
i
n
u
p
dat
e
_coor
d
s
commit
|
commitdiff
|
tree
2019-07-01
Pascal Me
r
z
Fix
module
detection for
p
h
y
sical validation
commit
|
commitdiff
|
tree
2019-06-24
P
a
s
cal Merz
Ma
k
e gl
o
bal t
o
pology
constant in traject
o
r
y
wri
t
ing
commit
|
commitdiff
|
tree
2019-05-27
P
ascal
Merz
Cle
a
n up
ren
a
med
si
m
ul
a
tor
.
h file
commit
|
commitdiff
|
tree
2019-05-25
Pascal M
e
rz
Remo
v
e
d
epend
e
nce
of mdou
t
f_wr
i
te_to_trajectory_
f
iles
.
.
.
commit
|
commitdiff
|
tree
2019-05-25
Pascal
M
erz
Rename Integrator class
commit
|
commitdiff
|
tree
2019-05-16
Pas
c
al
Me
r
z
Use
P
y
thon 3
commit
|
commitdiff
|
tree
2018-12-10
Pascal Merz
Fai
l
p
ro
o
f signal con
v
ersion
commit
|
commitdiff
|
tree
2018-09-26
Pas
c
al
Merz
(
R
e-)fix typo in DD load balancing printing
commit
|
commitdiff
|
tree
2018-09-25
P
a
s
cal
M
e
rz
Remove obsolete brac
e
s in do_
m
d()
commit
|
commitdiff
|
tree
2018-09-25
Pascal
M
erz
Rem
o
v
e
rerun from d
o
_md
commit
|
commitdiff
|
tree
2018-09-25
Pascal
Merz
Rem
o
ve unnecessary f
u
nctional
i
ty fro
m
do_r
e
run
commit
|
commitdiff
|
tree
2018-09-25
Pascal
M
erz
Pr
e
pare
r
er
u
n co
m
mi
t
commit
|
commitdiff
|
tree
2018-09-21
Pascal Merz
M
a
ke CGLO_CHECK_NUMBER_O
F
_BONDED_INTERACTIO
N
S requi
r
e
.
.
.
commit
|
commitdiff
|
tree
2018-09-18
P
ascal Merz
Docum
e
ntation fix:
Rerun
a
nd nstlist
commit
|
commitdiff
|
tree
2018-09-18
Pascal Merz
Intr
o
du
c
e
stop handler
commit
|
commitdiff
|
tree
2018-09-18
Pa
s
ca
l
Merz
I
ntrodu
c
e checkpoint handler
commit
|
commitdiff
|
tree
2018-09-18
P
ascal Merz
Introduce re
s
e
t han
d
ler
commit
|
commitdiff
|
tree
2018-09-17
Pas
c
a
l Merz
Fi
x
typ
o
in DD loa
d
ba
l
a
ncing p
r
inting
commit
|
commitdiff
|
tree
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