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Merge branch release-2018
2018-03-21
D
avid van der Spoe
l
Renamed e
n
t
ropy
.
* to thermoch
e
mistry
.
*
commit
|
commitdiff
|
tree
2018-03-16
David van der Spoel
Spl
i
t off e
n
tro
p
y ca
l
culation to separat
e
file
.
commit
|
commitdiff
|
tree
2017-12-28
David van
d
er
S
poe
l
Fi
x
es and updates f
o
r
xplor2gml
.
pl an
d
ato
m
_nom
.
tbl
commit
|
commitdiff
|
tree
2017-11-06
David van der Spoel
Fixe
d
check f
o
r
w
ater
in
gen_vsite
.
cpp
commit
|
commitdiff
|
tree
2017-11-02
D
avid van
de
r
Sp
o
e
l
New m
d
p inp
u
t for el
e
ctric field
s
.
commit
|
commitdiff
|
tree
2017-10-30
Davi
d
va
n
der S
p
o
el
F
i
xed mdp ou
t
put
f
ro
m
ele
c
tric field
c
ode
.
commit
|
commitdiff
|
tree
2017-10-30
D
avid van
d
er Spoel
Added
o
p
t
ion -water tips3p
t
o
pd
b
2gmx
.
commit
|
commitdiff
|
tree
2017-10-23
Davi
d
van der Sp
o
el
Split off the NMR relat
e
d
analyses fro
m
gm
x
e
n
erg
y
.
commit
|
commitdiff
|
tree
2017-10-17
David van de
r
S
p
oel
Fixed
mis
s
ing entries
in nrnb arrays
.
commit
|
commitdiff
|
tree
2017-08-15
David van der Spoel
W
o
rked around mi
s
s
ing OpenMP
i
mplementation in orires
.
commit
|
commitdiff
|
tree
2017-08-03
David va
n
d
er Spoel
Fixed bug in g
m
x
d
isres indexing
a
rra
y
s
.
commit
|
commitdiff
|
tree
2017-08-02
David van d
e
r Spo
e
l
W
o
rked around missing
Ope
n
M
P
implementa
t
ion in orir
e
s
.
commit
|
commitdiff
|
tree
2017-07-28
D
avid van der Spoel
Ad
d
ed unit-test for o
r
ienta
t
ion restraints output
.
commit
|
commitdiff
|
tree
2017-07-19
D
avid van der
Spoel
Remo
v
ed unnecessar
y
stati
c
decla
r
ations for command
.
.
.
commit
|
commitdiff
|
tree
2017-07-19
David van der Spoel
Fixed test-ord
e
r dependency in gmxprepro
c
ess tests
.
commit
|
commitdiff
|
tree
2017-07-19
Da
v
id va
n
der
Spoel
Fix
n
on-rep
r
oducability of clustsize te
s
ts
.
commit
|
commitdiff
|
tree
2017-05-01
David van der Spoel
X
p
m
test for gmx clust
s
ize
commit
|
commitdiff
|
tree
2017-03-12
David van
d
er Spoel
Added t
e
sts
f
or gmx clus
t
size
.
commit
|
commitdiff
|
tree
2017-03-04
David van d
e
r Spoel
Remove
s
r
o
gue printing
t
o xvg file in
gmx min
d
ist
commit
|
commitdiff
|
tree
2017-02-27
Dav
i
d van der Spoel
Fixes
bug
i
n
gmx solvate
w
i
t
h
-she
l
l that yielded 0
.
.
.
commit
|
commitdiff
|
tree
2017-02-03
David van der Spoe
l
Fixes SEGV in gmx ord
e
r
.
commit
|
commitdiff
|
tree
2017-02-02
David van d
e
r
Sp
o
e
l
Only prin
t
all dangling atom
s
with gromp
p
-v
commit
|
commitdiff
|
tree
2017-01-23
David
van der Spoel
Added ref
e
re
n
ce f
o
r dihedral function in OP
L
S
.
commit
|
commitdiff
|
tree
2016-12-07
Da
v
id van de
r
Spoel
C
o
u
p
l
e of n
e
w
quotes
commit
|
commitdiff
|
tree
2016-11-18
D
a
vid van der Spoel
A
d
ded first tests
o
f b
o
nded force functions
.
commit
|
commitdiff
|
tree
2016-10-14
David van der Spoel
F
ix
e
s some memory leaks associated
wi
t
h
testing applied
.
.
.
commit
|
commitdiff
|
tree
2016-10-07
David van
d
er Spoel
Modul
a
r
i
ze
e
lectric fiel
d
handli
n
g
commit
|
commitdiff
|
tree
2016-09-27
D
a
v
id van
der Spoel
F
ixed script
x
plor2gmx
.
p
l
t
o
work with GMXDATA
commit
|
commitdiff
|
tree
2016-09-26
David v
a
n der
S
poel
Fixes i
s
s
ue with Release build in
c
o
rr
e
lation functions
.
commit
|
commitdiff
|
tree
2016-09-20
David van der Spoel
Made correlation funct
i
on ro
u
tine use std::v
e
ctor
commit
|
commitdiff
|
tree
2016-09-05
David van der Spoel
Me
r
ge "Merge b
r
an
c
h release
-
2016"
commit
|
commitdiff
|
tree
2016-08-24
David van der S
p
o
e
l
Added
do
c
umentation
f
or
s
he
l
l
potentials
.
commit
|
commitdiff
|
tree
2016-08-03
David van de
r
Spoel
T
hree
n
ew quotes
.
commit
|
commitdiff
|
tree
2016-07-31
David
van der
Spoel
Merge "Merg
e
b
r
anch
rel
e
ase-5
-
1
i
nto release-2016"
.
.
.
commit
|
commitdiff
|
tree
2016-07-29
David va
n
der Spo
e
l
Fixes i
n
correct
c
har
g
es in OPLS
/
AA-L for HIS
D
and HISE
commit
|
commitdiff
|
tree
2016-07-08
D
avid van der Spoel
Merge
"
Merge b
r
an
c
h release-5-1 in
t
o
r
ele
a
se-2
0
16"
.
.
.
commit
|
commitdiff
|
tree
2016-07-08
D
a
vid van der Spoel
Int
r
oduce fatal
e
rror for
to
o
few frames in gmx do
s
.
commit
|
commitdiff
|
tree
2016-06-27
David van
der Spoel
M
a
de
g
mx dos wor
k
again
.
commit
|
commitdiff
|
tree
2016-06-22
David van der Spoel
R
e
moved
s
pu
r
ious r_i
j
in force for Mo
r
se
p
otential
.
.
.
commit
|
commitdiff
|
tree
2016-05-08
D
a
v
id van der Sp
o
el
Modify lmfit library to avoid
clashes with other
versi
o
ns
.
commit
|
commitdiff
|
tree
2016-03-23
Davi
d
v
a
n
d
er Spoel
Re
m
oved
srenew tha
t
was making array
s
m
aller in
c
orrectly
.
commit
|
commitdiff
|
tree
2016-03-18
Davi
d
v
a
n der Spoel
Fi
x
ed division by zero in polarize
.
commit
|
commitdiff
|
tree
2016-01-20
David van der S
p
oel
C
ouple of new quotes
commit
|
commitdiff
|
tree
2016-01-07
David van der Spoe
l
M
a
de normal modes work
w
ith shells
and
v
s
ites
commit
|
commitdiff
|
tree
2015-11-24
David
van der Spo
e
l
Fixes
newly intro
d
u
c
ed b
u
g in make_ndx
.
commit
|
commitdiff
|
tree
2015-11-23
David van der Spoel
Moved domdec
s
t
r
uctures out of commrec
.
h
.
commit
|
commitdiff
|
tree
2015-11-22
David van der Spoel
Cleanups in legacy
h
eader/types/
c
ommrec
.
h
commit
|
commitdiff
|
tree
2015-11-21
D
a
vid v
a
n d
e
r Spoel
Merged leg
a
c
yheaders/type
s
/qmmmrec
.
h into mdlib/qmmm
.
h
commit
|
commitdiff
|
tree
2015-11-21
David van der Spoel
Merg
e
d ge
n
bor
n
.
h fr
o
m legacy
h
ead
e
rs/ty
p
es
i
n
t
o
m
d
lib
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
Davi
d
van der Spoel
M
o
ve
d
l
e
g
a
cyhe
a
d
ers/
t
y
pes/group
.
h
to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoel
M
erged le
g
a
c
yheaders/typ
e
s/ns
.
h a
n
d
n
blist
.
h to
m
dtyp
e
s
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
D
avid van der Spoel
Combine enums
.
h and names*
.
commit
|
commitdiff
|
tree
2015-11-20
David van
d
e
r Spo
e
l
Merged legacyheader
s
/nrn
b
.
h and typ
e
s/nrnb
.
h
t
o gmxlib
.
commit
|
commitdiff
|
tree
2015-11-20
Dav
i
d van der
S
poel
Moved
m
d
ato
m
.
h from le
g
acyhead
e
r/
t
ypes to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-20
D
a
v
id van der Spo
e
l
Moved le
g
a
cyh
e
a
d
er
s
/
t
ypes/energy
.
h
to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-15
David van der
S
p
o
el
Merg
e
d le
g
acyheader
s
/typ
e
s/inputrec
.
h in
t
o mdtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-15
D
a
vid van
der
Spoel
M
e
rge
d
legacyh
e
aders/types/s
t
a
t
e
.
h into mdtypes/state
.
h
commit
|
commitdiff
|
tree
2015-11-13
D
av
i
d van der Spoel
Repl
a
ced
atom_id by int
.
commit
|
commitdiff
|
tree
2015-11-13
David van
d
er
S
poel
M
oved
gen
b
orn
.
h to
mdlib
commit
|
commitdiff
|
tree
2015-11-12
David v
a
n de
r
Spoel
Moved txtdump
.
* to fil
e
i
o
.
commit
|
commitdiff
|
tree
2015-11-12
David van der
S
p
o
el
M
o
v
e
d co
p
y
r
i
t
e
.
* to fileio fr
o
m gmxlib and legacyheaders
.
commit
|
commitdiff
|
tree
2015-11-11
D
avid van der Spoel
Moved inputrec
.
* from gmxlib and
l
egacyheader
s
to mdtype
s
.
commit
|
commitdiff
|
tree
2015-11-10
Da
v
id van der Spoel
Re
m
oved legacyheaders/
t
ypedefs
.
h
commit
|
commitdiff
|
tree
2015-11-03
David van der
Spoel
Moved df_histor
y
utili
t
y ro
u
tine
s
from typedefs to
.
.
.
commit
|
commitdiff
|
tree
2015-11-01
Da
v
id van der Spoel
Replace
d
NOTS
E
T from typedefs
.
h by l
o
cal solution
s
.
commit
|
commitdiff
|
tree
2015-10-23
Davi
d
van
der Sp
o
el
R
emoved energy
h
i
s
tory cod
e
fr
o
m
typedefs to a sepa
r
ate
.
.
.
commit
|
commitdiff
|
tree
2015-10-18
D
av
i
d van der
Spoel
M
oved pbc/cut-off
relate
d
ut
i
lities from typedef
s
to
.
.
.
commit
|
commitdiff
|
tree
2015-10-15
David
van der Spoel
Freed
memo
r
y
i
n
legac
y
sta
t
i
stic
s
routines
.
commit
|
commitdiff
|
tree
2015-10-03
D
av
i
d van der Spoel
Removed
s
imp
l
e
.
h
commit
|
commitdiff
|
tree
2015-10-02
David v
a
n der
Spo
e
l
Removed
simple
.
h from
n
b_ke
r
nel
_
sse4_1_X
X
commit
|
commitdiff
|
tree
2015-10-02
David van der Spoel
Removed simple
.
h
f
rom
n
b_ke
r
nel_sse2_XX
commit
|
commitdiff
|
tree
2015-10-02
Davi
d
van der Spoel
Remov
e
d simple
.
h from nb_ker
n
e
l_c and nb_ker
n
el_sparc64
_
hpc
.
.
.
commit
|
commitdiff
|
tree
2015-10-02
David van
d
e
r
Spoel
Remov
e
d inc
l
u
d
e simple
.
h from nb_kernel_a
v
x_128
_
fma_XX
commit
|
commitdiff
|
tree
2015-10-02
David van
de
r
Spoel
Remo
v
ed si
m
ple
.
h
f
rom nb_kernel_avx_25
6
_XX
commit
|
commitdiff
|
tree
2015-10-02
D
a
vid va
n
der S
p
oel
Removed output_env_t, now usin
g
gmx_output_env_t *
.
.
.
commit
|
commitdiff
|
tree
2015-10-01
D
avid van der Spo
e
l
Removed ty
p
e
s
/nrnb
.
h
f
rom typ
e
de
f
s
.
h
.
commit
|
commitdiff
|
tree
2015-09-30
David van der Spoel
Removed types/n
b
list
.
h a
n
d types/
n
sg
r
id
.
h
fr
o
m typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-30
D
avid van der Spoe
l
Removed types/mdatom
.
h from t
y
p
e
defs
.
h
commit
|
commitdiff
|
tree
2015-09-29
Da
v
id va
n
der Spoel
Removed
t
yp
e
s/inputre
c
.
h fro
m
t
y
pedefs
.
h and re
l
eted
.
.
.
commit
|
commitdiff
|
tree
2015-09-29
David v
a
n der Spoel
F
i
xes b
u
g in th
e
co
m
putation
o
f
C
oefficient of T
h
e
r
ma
l
.
.
.
commit
|
commitdiff
|
tree
2015-09-27
David van der S
p
oel
R
e
m
o
ved types/fo
r
cerec
.
h from typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-25
David van der Spoel
Re
m
oved inclu
d
e of types/i
f
unc
.
h fr
o
m type
d
efs
.
h
commit
|
commitdiff
|
tree
2015-09-22
David v
a
n
der Sp
o
el
Remo
v
ed four i
n
clude
s
from
l
egacyhea
d
er
s
/typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-22
D
a
v
id v
a
n de
r
Sp
o
el
Removed lega
c
y
headers/type
s
/commrec_fwd
.
h
from ty
p
edef
.
h
commit
|
commitdiff
|
tree
2015-09-10
David
v
an
der Spoel
Move
d
content from mdrun
.
h to separate h
e
ad
e
rs
.
commit
|
commitdiff
|
tree
2015-09-10
D
avid van der Spoel
R
emoved
<
sys
/
types
.
h> a
n
d "types/constr
.
h" f
r
om ty
p
edefs
commit
|
commitdiff
|
tree
2015-09-09
David van der
S
poel
Removed file
i
o/
t
rx
.
h from typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-08
David van der Spoel
Moved fu
n
ctions ope
r
ating
o
n forcerec to separate header
.
commit
|
commitdiff
|
tree
2015-08-28
David van der Spoel
A
dded energ
y
(ed
r
) fil
e
type to Options headers
.
commit
|
commitdiff
|
tree
2015-08-28
D
avid van
d
e
r Spoel
Add
e
d add
i
tional constructor t
o
S
t
ringStream class
.
.
.
commit
|
commitdiff
|
tree
2015-08-03
David v
a
n der
Spoel
Made
outp
u
t from dump
i
ng
n
e
i
ghtborlists easier to r
e
a
d
.
commit
|
commitdiff
|
tree
2015-07-31
David van der Spo
e
l
Change initial parame
t
ers for testing exp
f
it
.
commit
|
commitdiff
|
tree
2015-07-29
David v
a
n der Spoel
Code for ch
e
cking
x
v
g
file
s
in testut
i
ls
.
commit
|
commitdiff
|
tree
2015-04-17
Da
v
id
v
an der Spo
e
l
Up
d
a
t
ed
exponential fitting to make it rob
u
st
.
commit
|
commitdiff
|
tree
2015-04-09
David van
d
er Spoe
l
Clarif
i
e
d
comments for time-depen
d
ent electric fields
.
commit
|
commitdiff
|
tree
2015-04-08
David van
d
er Spoel
Fixed in
c
o
rrect o
u
tput o
f
gb_algorith
as
s
a_algorithm
.
commit
|
commitdiff
|
tree
2015-03-02
D
avid van
d
e
r Spoel
Up
d
ated documentation for
electric fields
.
commit
|
commitdiff
|
tree
2014-12-13
David
van der Spo
e
l
Four new quotes from
around the world
.
commit
|
commitdiff
|
tree
2014-11-28
David v
a
n der Spoel
Fi
x
es recently introdu
c
ed bug in
g
m
x an
a
lyze
.
commit
|
commitdiff
|
tree
2014-11-24
Da
v
id
van der Spoe
l
Ad
d
ed warnings for ewald-geometry and
s
urface
-
epsilon
commit
|
commitdiff
|
tree
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