Ri

phahI
nter
nat
ional
Uni
ver
sit
yFai
sal
abad

1
Comput
erPr
ogr
ammi
ng:

I
ntr
oduct
ion:

Ati
tsmostbasi
clev
el,comput
erpr
ogr
ammi
ngsi
mpl
ymeanst
ell
i
ngt
hecomput
er
whatt
odoandt
her
api
dsoundi
ngdef
ini
ti
oni
snotev
enaj
oke.Ther
ear
enoot
hert
rul
y
f
undament
alaspect
sofcomput
epr
ogr
ammi
ng;ev
ery
thi
ngel
sewet
alkaboutwi
l
l
si
mpl
ybet
hedet
ail
sofapar
ti
cul
ar,
usual
l
yar
ti
fi
cialmechani
sm f
ort
ell
i
ngacomput
er
whatt
odo.Somet
imest
hesemechani
smsar
echosenbecauset
heyhav
ebeenf
ound
t
obeconv
eni
entf
orpr
ogr
ammer
s(peopl
e)t
ouse;ot
hert
imest
heyhav
ebeenchosen
becauset
heyar
eeasyf
ort
hecomput
ert
ounder
stand.Thef
ir
sthar
dthi
ngabout
pr
ogr
ammi
ng i
stol
ear
n,become comf
ort
abl
e wi
th and acceptt
hese ar
ti
fi
cial
mechani
sms,
whet
hert
heymakesenset
oyouornot
.

I
nfact
,itdoesn’
tmat
terofsome (
orev
en many
)oft
he mechani
sms used f
or
pr
ogr
ammi
ngacomput
erdon’
tmakesense.Af
teral
l
,itdoesn’
tmakesenset
hatt
he
col
dwat
erf
aucethast
obeont
her
ightsi
deandt
hehi
tonehast
obeont
hel
eft
;of
cour
se,t
hati
sjustt
heconv
ent
ion wehav
eset
tl
ed on.On a si
mil
arnot
e,many
comput
erpr
ogr
ammi
ngmechani
smsar
equi
tear
bit
rar
yandwer
echosennotbecause
ofanyt
heor
eti
calmot
ivat
ionbutsi
mpl
ybecauseweneededanunambi
guouswayt
o
saysomet
hingt
oacomput
er.

Pr
ogr
ammi
ngr
equi
resmai
nlyal
ogi
calsenseofr
easoni
ng;anabi
l
ityt
osuppl
yasetof
i
nst
ruct
ions (
thepr
ogr
am)sot
hatt
hecomput
ercanexecut
ethem.I
ntheear
lyday
sof
comput
erpr
ogr
ammi
ng,
speci
ali
stsusedal
anguagenowcal
l
edl
owl
evelpr
ogr
ammi
ng
l
anguaget
ocommuni
cat
ewi
tht
hecomput
er.Thi
slanguagei
sver
ymuchl
i
keasetof
i
nst
ruct
ionsgi
veni
nbi
nar
yar
it
hmet
ic.Fori
nst
ance,dur
ingf
ir
stgener
ati
oncomput
er
pr
ogr
ammi
ngwast
edi
oussi
ncei
twasdonei
nmachi
nel
anguage.

Dur
ingsecondgener
ati
on,pr
ogr
ammi
ngwasdonei
nsy
mbol
i
c(assembl
ylanguage)
r
athert
hanmachi
nel
anguage.Assembl
ylanguagei
nvol
vest
heuseofmnemoni
csi
n
wr
it
ingpr
ogr
am.At
ransl
atorcal
l
edAssembl
erwasputi
npl
acet
otr
ansl
atepr
ogr
am
wr
it
teni
nassembl
ylanguagei
ntomachi
nel
anguagei
nst
ruct
ioncode.Thi
sgener
ati
on
waschar
act
eri
zedbyt
heuseoft
ransi
stor
.Theuseofhi
gh-
lev
ell
anguagesi
nwr
it
ing
pr
ogr
amscameaboutshor
tl
yaf
tert
hezeni
thoft
hesecondgener
ati
on.Thi
sinv
olv
es
t
he use ofEngl
i
sh l
i
ke t
erms i
n wr
it
ing pr
ogr
ams.Fr
om 1966 t
il
ldat
e,sev
eral

2
pr
ogr
ammi
nghav
ebeeni
nvent
edamongwhi
char
eFORTRAN,COBOL,BASI
C,C,C++,
JAVALet
c.

CONCEPTOFCOMPUTERPROGRAMMI
NG:

Theconceptofcomput
erpr
ogr
ammi
ngi
sacr
ossf
ert
il
izat
ionoft
wot
erms”Comput
er
and Pr
ogr
ammi
ng.A comput
eri
s an el
ect
roni
c dev
ice t
hatoper
ates undert
he
i
nst
ruct
ion&ast
oredpr
ogr
am,
accept
sinput
s(dat
a),
processesi
taccor
dingspeci
fi
ed
r
ules,pr
oducesout
put(
inf
ormat
ion)andst
orest
her
esul
tforf
utur
euse.Acomput
er
sy
stem i
smadeupoft
womai
npar
ts:
har
dwar
eandSof
twar
e.Har
dwar
eist
hephy
sical
componentofcomput
erwhi
l
esof
twar
eisaser
iesofi
nst
ruct
ionst
hatt
ellhar
dwar
e
howt
oper
for
mtasks.

Apr
ogr
am i
ncl
udesal
lthei
nst
ruct
ionsanddat
a,whi
chmustbepr
ovi
dedt
ocar
ryouta
gi
ven,assi
gnment
.Iti
sasetofi
nst
ruct
ionswr
it
teni
nacodi
fi
edf
orm,whi
chenabl
es
t
hecomput
ert
ocar
ryouti
tsoper
ati
onalact
ivi
ti
es.Apr
ogr
am coul
dal
sober
efer
redt
o
assof
twar
e.Thepr
ocessofpr
epar
ingsuchpr
ogr
am i
scal
l
edpr
ogr
ammi
ng.Comput
er
pr
ogr
ammi
ngi
sthepr
ocessofwr
it
teni
nst
ruct
ionst
ogui
decomput
eroper
ati
ons.I
t
i
nvol
vesast
ep-
by-
stepl
i
stofi
nst
ruct
ionswr
it
tenf
orpar
ti
cul
arcomput
erar
chi
tect
ure
i
napar
ti
cul
arcomput
erpr
ogr
ammi
ngl
anguage.

NGPROCE
COMPUTERPROGRAMMI SS:

Comput
erpr
ogr
am i
sast
ep-
by-
stepl
i
stofi
nst
ruct
ionswr
it
tenf
orpar
ti
cul
arcomput
er
ar
chi
tect
urei
napar
ti
cul
arcomput
erpr
ogr
ammi
ngl
anguage.A l
aymanequi
val
ent
exampl
ewi
l
lbewr
it
ingast
ep-
by-
stepl
i
stofi
nst
ruct
ionsi
nEngl
i
sh,i
nst
ruct
inga
st
udentt
oregi
sterf
orcour
sesf
ort
heacademi
csessi
on(
thehumanbei
ngt
hespeci
fi
c
ar
chi
tect
ure)
.Mor
eof
tent
hannotcc.
npupr
ogr
amsar
ecompi
l
edorassembl
edi
nto
non-
humanf
ormat
.Inot
herwor
ds,
comput
erpr
ogr
am canal
sobesai
dtoapr
ocessof
t
aki
ng t
hest
epsi
n a pr
ocedur
eand put
ti
ng t
hem i
nthecoded l
anguageoft
he
comput
er.

I
nthe pr
ocess pr
oduci
ng t
he necessar
yinst
ruct
ions maki
ng up a pr
ogr
am,t
he
f
oll
owi
ngst
agescanber
ecogni
zedascanbeseeni
nthedi
agr
am bel
ow:

1)Under
standi
ngt
hePr
obl
em:

3
 Thi
sist
hef
ir
stst
agei
ntr
yingt
owr
it
eapr
ogr
am.Att
hisst
age,t
hepr
obl
em i
s
i
dent
if
ied,
anal
yzedandmustbepr
oper
lyunder
stood.

2)Pl
anni
ngt
heMet
hodofSol
uti
on:

Af
terunder
standi
ngt
hepr
obl
em t
obesol
ved,pl
ansar
emadeonwhatmet
hod
t
ogoaboutsol
vi
ngt
hepr
obl
em.

3)Wr
it
ingt
heI
nst
ruct
ioni
naPr
ogr
ammi
ngLanguage:

Att
hisst
aget
hepr
ogr
ammerwi
l
lsel
ectt
hepr
ogr
am l
anguaget
hatbestsui
ts
hi
sorherr
equi
rement
sThei
nst
ruct
ioncanbewr
it
teni
nhi
ghl
evell
anguage,
low
l
evel
language,
lowl
evel
machi
necode(
language)
.

4)Tr
anscr
ibi
ngt
heI
nst
ruct
ioni
ntoaMachi
neSensi
blef
orm:

Thi
sisal
soknownast
hecompi
l
ati
onst
age.Apr
ogr
am whi
chhasbeenwr
it
ten
i
nahi
ghl
evel
languagemustei
therbe:

 Compi
l
edi
ntoamachi
necodef
orm,
fori
nputi
ntot
hecomput
er.

 I
nputi
ntoi
tsexi
sti
ngf
orm t
othecomput
er,whi
chwi
l
ltr
ansl
atet
he
i
nst
ruct
ioni
ntomachi
necodef
orm usi
ngani
nter
pret
er.

5)Test
ingt
hePr
ogr
am:

Att
hisst
aget
hepr
ogr
am t
hathasbeenwr
it
tenwi
l
lhav
etobet
est
ed.The
pr
ogr
ammermustt
estt
heobj
ectpr
ogr
am wi
tht
het
estdat
a.A di
agnost
ic
r
out
ineordebuggi
ngr
out
inepr
ovi
desf
orr
out
inepr
ogr
am t
est
ingander
ror
cor
rect
iondur
ingpr
ogr
am dev
elopment
.Whent
hepr
ogr
am doesnotr
unwel
l
,
t
heer
rormustbel
ocat
ed.Di
agnost
icr
out
inewi
l
lfi
ndoutwhatt
hepr
ogr
am was
doi
ngatt
het
imei
tfai
l
ed,andwhatt
hecont
ent
sofst
orewer
e.Testpacksar
e
usedt
otestt
heef
fect
ivewor
kingofnew comput
erpr
ogr
amsbef
oret
heyar
e
usedoper
ati
onal
l
y.

6)Document
ingal
lthewor
kinv
olv
edi
npr
oduci
ngt
hePr
ogr
am:

4
 St
art
ingf
rom t
hepoi
ntofunder
standi
ngt
hepr
ogr
am t
obesol
ved,t
othepoi
nt
wher
ethepr
ogr
am becomesef
fect
ivei
sdocument
ed.

7)Mai
ntenanceoft
hePr
ogr
am:

Att
hisst
aget
hewor
kabl
epr
ogr
am mustmai
ntai
ned.Thi
sisi
mpor
tantbecause
t
hecomput
erusermaydeci
det
hatIpr
ogr
am oughtt
obecapabl
eofdoi
ng
addi
ti
onal
processi
ngr
out
ineorsi
xpr
ocesssomedat
ainadi
ff
erentway
.

FEATURESOFAGOODCOMPUTERPROGRAM:

Thef
oll
owi
ngar
esomechar
act
eri
sti
csofagoodcomput
erpr
ogr
am.

1)Rel
i
abi
l
ity
:Thi
schar
act
eri
sti
cimpl
i
est
hatt
hepr
ogr
am canbedependedupon
al
way
stoper
for
m ef
fi
cient
ly.

2)Mai
ntai
nabi
l
ity
:Thati
sthepr
ogr
am shoul
dbeeasi
l
ymodi
fi
edandupdat
edwhent
he
needar
ises.

3)Pr
ofi
tabi
l
ity
:Thati
sthepr
ogr
am shoul
dwi
l
lbet
ransf
erabl
etoadi
ff
erentcomput
er
wi
thl
i
ttl
eornomodi
fi
cat
ion.

4)Readabi
l
ity
:Thi
sist
osayt
hepr
ogr
am shoul
dbeeasyf
orapr
ogr
ammet
oreadand
under
stand.

5)Per
for
mance:Thepr
ogr
am shoul
dbecapabl
eofcausi
ngt
het
askt
obeper
for
med
qui
ckl
yandef
fi
cient
ly.

6)St
orageSav
ing:
Thepr
ogr
am shoul
dnotbeal
l
owedt
obeunnecessar
yal
ong.

COMPUTERPROGRAMMI
NGLANGUAGE:

Pr
ogr
ammi
ngl
anguagesar
evar
iousbywhi
cht
hepr
ogr
amsar
ewr
it
ten.Eachpr
ogr
am
i
swr
it
teni
napar
ti
cul
arl
anguage,butt
her
ear
equi
teal
argenumberofdi
ff
erent
l
anguages,j
ustasspokenl
anguagesi
ncl
udeEngl
i
sh,Fr
ench,Ger
man,Russi
aand
Cant
oneseandsoon.Whenapr
ogr
am i
swr
it
ten,i
tiswr
it
teni
napr
ogr
ammi
ng
l
anguage.Thi
sisnei
thert
henor
malwr
it
tenl
anguageofhumans,nori
tisusual
l
ythe
machi
necodel
anguageofcomput
ers.

TYPESOFPROGRAMMI
NGLANGUAGES:
5
Pr
ogr
ammi
ngl
anguagescanbegr
oupedi
nto3br
oadcat
egor
iesv
iz:

 Lowl
evel
languages

 Hi
ghl
evel
languages

 Four
thgener
ati
onl
anguages

LowLev
elLanguage:

Thesel
anguagesconsi
stofmachi
neassembl
ylanguage.

a.Machi
ne Language:I
tfor
ms t
he ear
li
erpr
ogr
am dev
eloped by t
he comput
er
pr
ogr
ammer
.Iti
sgener
ati
on.I
tusest
hebi
nar
ycodesi
ndi
git
sofzer
oandi
nmachi
ne
codes(
languages)wasusual
l
yver
ycompl
ex,
prone,
duet
othef
actt
hatev
erypr
ogr
am
mustbei
nthecodes(
language)bef
oreanyt
askcanbeexecut
ed.

b.Assembl
yLanguage:Assembl
ylanguagewasaf
rom machi
necode(
language)
.Thi
s
i
samachi
nespeci
fi
clanguage,butt
het
askofl
ear
ningandwr
it
ingt
hel
anguagei
s
madeeasi
ert
hanwi
tht
hemachi
necode(
language)
,becausei
tiswr
it
teni
nsy
mbol
i
c
f
orm.i
nst
eadofusi
ngmachi
necode(
language)oper
ati
onnumber
s,t
hepr
ogr
ammeri
s
abl
etousel
ear
nedandunder
stoodoper
ati
onmnemoni
cs(
forexampl
e,ADD,SUB,
MULTet
c)andsy
mbol
i
cdat
alocat
ions(
namesal
l
ocat
edbyt
hepr
ogr
ammerandused
t
oref
ert
opar
ti
cul
ardat
aar
easi
nthepr
ogr
am)r
epl
acenumer
icdat
alocat
ions.

2.Hi
ghLev
elLanguages:Thesear
ecal
l
edt
hir
dgener
ati
onl
anguages.Thesear
e
machi
nei
ndependentl
anguagewhi
chmeanst
heyar
ecompat
ibl
ewi
thanyt
ypeof
machi
ne.Thi
sgener
ati
onofcomput
erl
anguagesusesext
ensi
vev
ocabul
aryofwor
ds
andsy
mbol
sar
eusedt
oinst
ructacomput
ert
ocar
ryoutt
henecessar
ypr
ocedur
es,
r
egar
dlessoft
het
ypeofmachi
nebei
ngsued(
alt
hought
hepr
ogr
am t
hatt
ransl
atesa
hi
ghl
evell
anguagei
ntoamachi
necodef
orm knownasacompi
l
erori
nter
pret
eri
s
di
ff
erentf
oreachmakeofcomput
er.

3.Four
thGener
ati
onLanguage:

Thi
sgener
ati
onofcomput
erl
anguagehaswi
tnessedamar
keti
mpr
ovementont
he
exi
sti
ngcomput
erl
anguages.Thi
sgener
ati
onofl
anguagei
slong,
procedur
alandmor
e
conv
ersi
onal
.The non-pr
ocedur
alaspectdenot
est
hatt
he usercan i
nst
ructt
he

6
comput
eronwhatheneedst
oachi
eveandt
hecomput
erwi
l
lgener
atet
hei
nst
ruct
ions
t
oachi
evet
her
esul
t.

Sof
twar
eusedi
nComput
ati
onal
Chemi
str
y:
Ev
eni
fyouhav
enotst
udi
edquant
um chemi
str
yindet
ail
,youpr
obabl
yhav
ereal
i
zed
t
hatat
ypi
calmol
ecul
armechani
cspr
obl
em i
samany
-bodypr
obl
em i
nwhi
chsev
eral
nucl
eiandmanyel
ect
ronsi
nter
actwhi
l
emov
ing.Ast
her
eisnoknownanal
yti
cal
,
cl
osedf
orm sol
uti
onst
osuchmany
-bodypr
obl
ems,onehast
orel
yonappr
oxi
mat
e
met
hodswhensol
vi
ngmol
ecul
arquant
um mechani
cspr
obl
ems.Thel
argenumberof
di
ff
erentquant
um mechani
cspr
ogr
amsi
spar
ti
all
yar
esul
tofdi
ff
erentr
esear
cher
s
f
ocusi
ng ef
for
ton di
ff
erentappr
oxi
mat
e sol
uti
ons ort
ryi
ng t
o descr
ibe di
ff
erent
aspect
sofmol
ecul
arbehav
iour
.Thus,eachpopul
arquant
um mechani
cspr
ogr
am has
somesetofst
rengt
hst
hatset
sitapar
tfr
om ot
herpr
ogr
ams.

Besi
desav
astandcont
inui
ngi
ncr
easei
ncomput
ati
onalpowerov
ert
hel
astdecades,
sof
twar
ehasbeendev
elopedt
odealwi
thl
argerandmor
ecompl
exsy
stems,
andmor
e
pr
oper
ti
es ar
e av
ail
abl
e.Comput
ati
onalchemi
str
ysof
twar
e wi
l
lst
rongl
yadv
ance
r
esear
ch bypr
ovi
ding i
nsi
ghti
nreact
ivi
tyand pr
oper
ti
es,and bypr
edi
cti
ng new
mol
ecul
es,mat
eri
alsorsol
ventmi
xtur
es.Especi
all
ybycombi
ningexper
iment
alwi
th
model
i
ngef
for
ts,
exper
iment
alcost
sandt
imecanber
educedandbet
terper
for
mance
achi
eved.

Dal
ton

 Focusonpr
edi
cti
ngpr
oper
ti
esofmol
ecul
es

 Mol
ecul
arpol
ari
zabi
l
iti
es

 Di
sper
sioncoef
fi
cient
s(v
anderWaal
spar
amet
ers)

DI
RCCR12

 Coupl
edcl
ust
ercal
cul
ati
onswi
thexpl
i
citel
ect
roncor
rel
ati
on

 Hi
ghl
yaccur
ateener
gies

Gaussi
an:

7
Basedont
hef
undament
all
awsofquant
um mechani
cs,
Gaussi
anal
l
owsy
out
opr
edi
ct
t
heener
gies,mol
ecul
arst
ruct
uresandv
ibr
ati
onalf
requenci
esofcompl
exmol
ecul
ar
sy
stems,andt
oant
ici
pat
ethei
rchemi
calpr
oper
ti
es.Mol
ecul
esandr
eact
ionscanbe
st
udi
edunderawi
der
angeofcondi
ti
onsnotonl
yforst
abl
especi
esorcompl
ex
compoundsbutal
sof
orexper
iment
all
yunobser
vabl
ecompounds,suchasephemer
al
i
nter
medi
atesort
ransi
ti
onst
ate

 Mol
ecul
armechani
cs

 Semi
-empi
ri
cal
quant
um chemi
str
ymet
hodcal
cul
ati
ons

 Bui
l
t-i
ndensi
tyf
unct
ional
theor
y(DFT)met
hods

 Br
oadr
angeofcommonl
yrequi
redQM model
sandf
eat
ures

 Suppor
tforQM/
MM v
iaONI
OM,
NMRpr
oper
ti
es,
UVci
rcul
ardi
chr
oism

Gamess

(
GAMESS(
US)
)iscomput
ersof
twar
eforcomput
ati
onalchemi
str
ypr
ogr
am.GAMESS
(
US)i
smai
ntai
nedbyt
hemember
soft
heGor
donResear
chGr
oupatI
owaSt
ate
Uni
ver
sit
y.GAMESS (
US)can per
for
m sev
eralgener
alcomput
ati
onalchemi
str
y
cal
cul
ati
ons,i
ncl
udi
ng Har
tree–Fock met
hod,densi
tyf
unct
ional t
heor
y(DFT)
,
gener
ali
zed v
alence bond (
GVB)
,and mul
ti
-conf
igur
ati
onalsel
f-
consi
stent f
iel
d
(
MCSCF)
.Itwasdev
elopedbyI
owaSt
ateUni
ver
sit
y.

 Br
oadr
angeofcommonl
yrequi
redQM model
sandf
eat
ures

 Env
ironmentdescr
ipt
ionv
iaef
fect
ivef
ragmentpot
ent
ial
s

 Renor
mal
i
zedcoupl
edcl
ust
erener
gies

Psi
3

PSI
3isapr
ogr
am sy
stem anddev
elopmentpl
atf
ormf
orabi
nit
iomol
ecul
arel
ect
roni
c
st
ruct
urecomput
ati
ons.Thepackagei
ncl
udesmat
urepr
ogr
ammi
ngi
nter
facesf
or
par
singuseri
nput
,accessi
ngcommonl
yuseddat
asuchasbasi
s-seti
nfor
mat
ionor
mol
ecul
aror
bit
alcoef
fi
cient
s,andr
etr
iev
ingandst
ori
ngbi
nar
ydat
a(wi
thnosof
twar
e
l
i
mit
ati
onsonf
il
esi
zesorf
il
e-sy
stem-
sizes)
,especi
all
ymul
ti
-i
ndexquant
it
iessuchas

8
el
ect
ronr
epul
si
oni
ntegr
als.Thi
spl
atf
ormi
susef
ulf
ort
her
api
dimpl
ement
ati
onof
bot
hst
andar
dquant
um chemi
cal
met
hods,
aswel
last
hedev
elopmentofnewmodel
s.

 Goodper
for
manceofcoupl
edcl
ust
ercal
cul
ati
ons

 Suppor
tforv
eryl
argebasi
sset
s

 Ef
fi
cientconf
igur
ati
oni
nter
act
ioncal
cul
ati
onsf
orchemi
cal
react
ions

SAMSON:

SAMSON(
Sof
twar
eforAdapt
iveModel
i
ngandSi
mul
ati
onOfNanosy
stems)i
soneof
t
hemostqui
ckl
ygr
owi
ngpl
atf
ormsf
ori
ntegr
atedmol
ecul
ardesi
gn.SAMSON’
sgoali
s
t
omakei
tfast
erf
orev
ery
onet
odesi
gndr
ugs,mat
eri
als,andnanosy
stems.I
tisbei
ng
dev
elopedbyOneAngst
rom andpr
evi
ousl
ybyt
heNANO-
Dgr
oupatt
heFr
enchI
nst
it
ute
f
orResear
chi
nComput
erSci
enceandAut
omat
ion(
INRI
A).

Jaguar

Jaguari
s a comput
ersof
twar
e package used f
orab i
nit
io quant
um chemi
str
y
cal
cul
ati
onsf
orbot
hgasandsol
uti
onphases.
Iti
scommer
cialsof
twar
emar
ket
edby
t
hecompanySchr
ödi
nger
.Oper
ati
ngsy
stemsar
eLi
nux
,Mi
crosof
tWi
ndows,
MacOSX.
Jaguarpr
oceedsmuchf
ast
ert
hanconv
ent
ionalabi
nit
iopr
ogr
ams,maki
ngi
tpossi
ble
t
ocar
ryoutmanymor
ecal
cul
ati
onswi
thi
nthesamet
imef
rame.

 Fastl
ocal
i
zedMP2cal
cul
ati
onsal
l
owsanal
ysi
sofl
argermol
ecul
es

 Easyt
ouseduet
oti
ghti
ntegr
ati
onwi
thMaest
roGUI

 Conf
ormat
ional
anal
ysi
s,sol
vat
ionf
reeener
gies

SAPT

Sy
mmet
ry-
adapt
edper
tur
bat
iont
heor
y(SAPT)pr
ovi
desameansofdi
rect
lycomput
ing
t
henoncov
alenti
nter
act
ionbet
weent
womol
ecul
es,t
hati
s,t
hei
nter
act
ionener
gyi
s
det
ermi
nedwi
thoutcomput
ingt
het
otal
ener
gyoft
hemonomer
sordi
mer
.

9
  I
nter
mol
ecul
arf
orces

 Di
sper
sioni
nter
act
ions

Mol
pro

Mol
proi
sacompr
ehensi
vesy
stem ofabi
nit
iopr
ogr
amsf
oradv
ancedmol
ecul
ar
el
ect
roni
cst
ruct
urecal
cul
ati
ons,desi
gnedandmai
ntai
nedbyH.
-J.Wer
nerandP.J.
Knowl
es,andcont
aini
ngcont
ri
but
ionsf
rom manyot
heraut
hor
s.I
tcompr
isesef
fi
cient
and wel
lpar
all
eli
zed pr
ogr
amsf
orst
andar
d comput
ati
onalchemi
str
yappl
i
cat
ions,
suchasDFTwi
thal
argechoi
ceoff
unct
ional
s,aswel
lasst
ate-
of-
thear
thi
gh-
lev
el
coupl
ed-
clust
erandmul
ti
-r
efer
encewav
efunct
ionmet
hods.Mol
proi
sver
yeasyt
ouse
f
orst
andar
d appl
i
cat
ions,butal
so i
ncl
udes many adv
anced opt
ions f
orexper
t
appl
i
cat
ions

 Mul
ti
ref
erencesy
stems,
descr
ipt
ionofchemi
cal
react
ions

 Pr
edi
cti
onofUV-
Visspect
ra

Spar
tan

Spar
tan i
s a mol
ecul
armodel
l
ing and comput
ati
onalchemi
str
y appl
i
cat
ion f
rom
Wav
efunct
ion.I
tcont
ainscodef
ormol
ecul
armechani
cs,semi
-empi
ri
calmet
hods,ab
i
nit
io model
s, densi
ty f
unct
ional model
s, post
-Har
tree–Fock model
s, and
t
her
mochemi
calr
eci
pesi
ncl
udi
ngG3(
MP2)andT1.Quant
um chemi
str
ycal
cul
ati
onsi
n
Spar
tanar
epower
edbyQ-
Chem.I
twasi
nit
ial
l
yrel
easedi
n1991.

I
tiswr
it
teni
nC,C++,For
tranandOt
.Li
nus,
macOSXandwi
ndowsar
eit
soper
ati
ng
sy
stems.
Iti
seasyt
ouseduet
owel
l
-bui
l
tGUI
.

 Av
ail
abl
eforWi
ndows,
LinuxandmacOSandi
nmanyl
anguages

 Suppor
tsmul
ti
-cor
ecomput
ati
ons

 Easyt
ounder
standandwor
k

 Easyt
ouseduet
owel
l
-bui
l
tGUI

 El
ect
roni
cst
ruct
ures,
conf
ormat
ional
anal
ysi
s

10
  Vi
sual
i
zat
ionofmol
ecul
arpr
oper
ti
es

ORCA:

ORCAi
sanabi
nit
ioquant
um chemi
str
ypr
ogr
am packagedev
elopedbyt
her
esear
ch
gr
oupofFr
ankNeeseatMaxPl
antI
nst
it
utei
n2012.Thi
spackagecont
ainsmoder
n
el
ect
roni
cst
ruct
ure met
hodsi
ncl
udi
ng DFT cal
cul
ati
ons,many
-bodyper
tur
bat
ions,
coupl
ed-
clust
ermet
hods,mul
ti
ref
erencemet
hods,andsemi
-empi
ri
calcal
cul
ati
ons.I
ts
mai
nfi
eldofappl
i
cat
ioni
slar
germol
ecul
es,t
ransi
ti
onmet
alcompl
exes,andt
hei
r
spect
roscopi
c pr
oper
ti
es.The f
ree v
ersi
on i
s av
ail
abl
e onl
yforacademi
c use at
academi
cinst
it
uti
ons.

NAMD

Nanoscal
eMol
ecul
arDy
nami
cs(
NAMD,i
nthepastNotAnot
herMol
ecul
arDy
nami
cs
Pr
ogr
am)i
sPCpr
ogr
ammi
ngf
orsub-
atomi
cel
ement
srecr
eat
ion,composedut
il
izi
ng
t
heChar
m++,equalpr
ogr
ammi
ngmodel
.Iti
snot
edf
ori
tssi
mil
arpr
oduct
ivi
tyandi
s
nor
mal
l
yusedt
oreenacthugef
ramewor
ks(
avastnumberofat
oms)
.Ithasbeen
cr
eat
edbyt
hej
ointef
for
toft
heTheor
eti
cal
andComput
ati
onal
Biophy
sicsGr
oup(
TCB)
and t
he Par
all
elPr
ogr
ammi
ng Labor
ator
y(PPL)att
he Uni
ver
sit
y ofI
ll
i
noi
s at
Ur
bana–Champai
gn.

Av
ogadr
o:

I
tisanopen-
sour
cesof
twar
eusedi
ncomput
ati
onalchemi
str
y,mol
ecul
armodel
i
ng,
bi
oinf
ormat
ics,
etc.I
twasf
ir
sti
ntr
oducedi
n2008andwr
it
teni
nC++l
anguage.

 Av
ail
abl
eforWi
ndows,
LinuxandmacOSandi
nmanyl
anguages

 Fr
eeandOpen-
sour
ce

 Suppor
tsmul
ti
-t
hreadedr
ender
ingandcomput
ati
on

 Easyt
ounder
standandwor
k

 Pl
ugi
nar
chi
tect
uref
ordev
eloper(
commands,
Pyt
honscr
ipt
s)

 Babel
chemi
cal
fil
eimpor
t

11
ChemDr
aw:

I
tisapar
ti
clemanageri
nit
ial
l
ycr
eat
edi
n1985byDav
idA.Ev
ansandSt
ewar
t
Rubenst
ein.

 Av
ail
abl
eforWi
ndows,
macOS

 Chemi
cal
str
uct
uret
onameconv
ersi
onandv
icev
ersa

 NMR&Massspect
rum si
mul
ati
on

 Expor
ti
ngt
odi
ff
.imagef
il
ety
pe

 NoLi
nuxv
ersi
on

 Commer
cial
sof
twar
e

12