Move cursor:
h: move cursor left
j: move cursor down
k: move cursor up
l: move cursor right
G: go to bottom of file
:# : go to line #
^G: tells you the line number of the current cursor line

Insert text:
i: insert before cursor (end with ESC)
a: append after cursor (end with ESC)
A: append at end of cursor line (end with ESC)
I: insert before first non-blank of cursor line (end with ESC)

Delete text:
x: delete character at current cursor position
dd: delete current line
#dd: delete # lines (starting with cursor line)
D: delete from cursor to end of line

Move text around:
yy: yank current cursor line (without deleting text)
#yy: yank # lines starting with cursor line (without deleting text)
p: put last deleted or yanked text after current cursor position

Search for a string:
/string: move cursor to next occurrence of string (in forward direction)
?string: move cursor to next occurrence of string (in backward direction)
n: repeat last / or ?

Substitute word2 for word1:
:1,$s/word1/word2/g: substitute for entire file
:s/word1/word2/: substitute for first appearance on current cursor line

Save and quit current file:
:w filename: write to filename (if same name, can omit filename)
:q :quit file
:q! :quit file without saving changes since last saved
:wq or ZZ: write file and quit

Insert another file into current file:
:r filename: insert filename into current file

Undo:
u: undo previous command

Beginning and end of program:
First line:
program name

Last line:
end

Declare variable types:
real*8
integer

Arithmetic operations:
addition: a+b
subtraction: a-b
multiplication: a*b
division: a/b
exponentiation: a**b

Priority of operations:
1. parentheses
2. exponentiation
3. multiplication and division
4. addition and subtraction
If 2 operations have the same priority, all operations except exponentiation are performed
left to right. Two sequential exponentiations are performed right to left.

Relations:
is equal to: .eq.
is not equal to: .ne.
is greater than: .gt.
is less than: .lt.
is greater than or equal to: .ge.
is less than or equal to: .le.

Input and output:
read(5,*) x,y,z
(5 indicates default input, * indicates default format for types x,y,z)

write(6,100) x,y,z
(6 indicates default output, 100 indicates line of format statement)

run program prog.x with input file in.dat and output file out.dat:
prog.x < in.dat > out.dat

Format:
Integers:
iw: w represents total width (number of positions)

Real numbers in decimal form:
fw.d: w represents total width (number of positions) including decimal point
d represents number of these positions to the right of the decimal point
f6.3: XX.XXX

Space:
x

Numbers are right-adjusted within the specified width w.
A preceding integer indicates the quantity of numbers of that type.

100 format(3f6.3) 3 real numbers of width 6 on one line
100 format(3i5) 3 integers of width 5 on one line
100 format(f6.3,2x,f6.3,2x,f6.3) 3 real numbers of width 6, each separated by 2 spaces

Loops:
do index=initial,limit
set of statements
enddo

do while condition
set of statements
enddo

if condition then
set of statements
endif

if condition then
set of statements
else
set of statements
endif

Arrays: (1-dimensional)
group of storage locations (row of data); each element is of the type declared at the beginning

Declaration:
real*8 ar(20)
integer ar(20)

Assignment of elements:
ar(1)=2.0
x=ar(2)

Input and output of elements:
read(5,*) ar(10)
write(6,100) ar(1),ar(2),ar(3)

Subroutines:

subroutine name(argument list)
set of statements
return
end

Call subroutine from main program:
call name(argument list)

Arguments in the call statement must match those in the subroutine.

Compile: (fortran code in prog.f, executable in prog.x)
f77 -o prog.x prog.f

Run: (input and output files in.dat and out.dat, respectively)
prog.x < in.dat > out.dat

Plot:
To get into program type:
xvgr (return)

To read in file and plot:
Go to Files pulldown and choose Read Sets
Choose your file from Contents, which should result in the following:
File: output.dat (the file you chose from Contents)
Change File type to be as follows:
File type: X Y1 Y2 ...
Use the defaults for the other options
Click on Accept and then on Done

Then go to View pulldown and choose Autoscale
Change Autoscale axis to be as follows:
Autoscale axis: All
Click on Accept and then on Done

To plot another file on the same axes, just repeat the above process to read in file and plot.

To print:
Go to Files pulldown and choose Print

To quit:
Go to Files pulldown and choose Exit

EXAMPLE PROGRAMS:
c These programs read in an initial value for r and the step size
c and prints out r and r**2 for 101 points

Sample input file:
-0.5
0.01
c Example of use of do loop, reading input, and writing output.
program testp1
real*8 r,step
integer i

read(5,*) r
read(5,*) step
do i=1,101
write(6,100) r,r*r
r=r+step
enddo
100 format(f9.5,x,f9.5)
end
*******************************************
c Example of use of 1-dimensional arrays.
program testp2
real*8 r,step,ar(200)
integer i

read(5,*) r
read(5,*) step
do i=1,101
ar(i)=r
r=r+step
enddo
do i=1,101
write(6,100) ar(i),ar(i)*ar(i)
enddo
100 format(f9.5,x,f9.5)
end
*******************************************
c Example of use of subroutines.
program testp3
real*8 r,step,ar(200)
integer i

read(5,*) r
read(5,*) step
call doloop(r,step,ar)
do i=1,101
write(6,100) ar(i),ar(i)*ar(i)
enddo
100 format(f9.5,x,f9.5)
end

subroutine doloop(r,step,ar)
real*8 r,step,ar(200)
integer i
do i=1,101
ar(i)=r
r=r+step
enddo
return
end

real*8 dt,r1,r2,v1,v2,m1,m2,f1,f2
real*8 dt2,dtsq2

dt2=dt/2.0
dtsq2=dt*dt2
r1=r1+dt*v1+dtsq2*f1/m1
v1=v1+dt2*f1/m1
r2=r2+dt*v2+dtsq2*f2/m2
v2=v2+dt2*f2/m2

return
end

c This subroutine is part 2 of the velocity Verlet algorithm, where
c dt is the time step. The velocities are moved from time t+dt/2
c to time t+dt.
subroutine moveb(dt,r1,r2,v1,v2,m1,m2,f1,f2)

real*8 dt,r1,r2,v1,v2,m1,m2,f1,f2
real*8 dt2

dt2=dt/2.0
v1=v1+dt2*f1/m1
v2=v2+dt2*f2/m2

return
end
end of md.f

The program md.f contains two subroutines for the velocity Verlet algorithm.
Write a program that does molecular dynamics for two particles (in 1-dimension) interacting with a harmonic oscillator potential (as in assignment #3).

Input file should be as follows:
r1 r2 (positions of 2 particles)
v1 v2 (velocities of 2 particles)
m1 m2 (masses of 2 particles)
ro
k
dt (time step)
nstep (number of MD steps)
Output file should contain 5 columns: time, distance between the two particles, potential energy, kinetic energy, total energy.

Hints:
The variables are declared as follows:
real*8 r1,r2,v1,v2,m1,m2,f1,f2,dt
real*8 k,ro,totenergy,kinenergy,potenergy
integer i,nstep

The statements in the program that read the input are:
read(5,*) r1,r2
read(5,*) v1,v2
read(5,*) m1,m2
read(5,*) ro
read(5,*) k
read(5,*) dt
read(5,*) nstep

The statement that writes out each line of the output is:
write(6,100) dt*i,r,potenergy,kinenergy,totenergy

The format statement is:
100 format(f9.5,x,f9.5,x,f9.5,x,f9.5,x,f9.5)

The force on each particle is calculated by:
r=dabs(r2-r1)
f1=-k*(r-ro)*(r1-r2)/r
f2=-k*(r-ro)*(r2-r1)/r
The kinetic energy is:
kinenergy=0.5*m1*v1*v1+0.5*m2*v2*v2
The potential energy is:
potenergy=0.5*k*(r-ro)**2
The total energy is:
totenergy=kinenergy+potenergy

The loop for the MD is as follows:
calculate force
do i=1,nstep
call movea(dt,r1,r2,v1,v2,m1,m2,f1,f2)
calculate force
call moveb(dt,r1,r2,v1,v2,m1,m2,f1,f2)
calculate kinetic energy
calculate potential energy
calculate total energy
write output
enddo

Turn in:
1. Copy of program
2. Copy of output file using input files input2a.dat, input2b.dat, and input2c.dat below
input2a.dat
-0.6 0.6
0.0 0.0
2.0 2.0
1.0
15.0
0.1
100

input2b.dat
-0.6 0.6
0.0 0.0
2.0 2.0
1.0
15.0
0.01
1000

input2c.dat
-0.6 0.6
0.0 0.0
2.0 2.0
1.0
30.0
0.01
1000

3. Plots of distance, kinetic energy, potential energy, and total energy as function of time for results from #2 (3 separate graphs (with 4 curves each) -- one for input2a.dat, one for input2b.dat, and one for input2c.dat) -- label curves and graphs!!!
4. Answer questions:
(a) When the distance r is at a minimum or maximum, is the kinetic energy at a minimum or maximum? How about the potential energy?
(b) When the distance r is at its equilibrium value (r=1.0 in this case), is the kinetic energy at a minimum or maximum? How about the potential energy?
(c) Does data set from input2a.dat or input2b.dat conserve total energy better? Why is this so?
(d) Do the potential and kinetic energies vary more for data set from input2b.dat or input2c.dat? Based on the graphs from Assignment #3, why is this so?

Hints:
Declare variables as follows:

write(6,100) v
The format statement is
100 format(f12.5)

Turn in:
1. Copy of your program with responses to #2 and #3 written on the top of the first page.
2. The result (just a number) of using input file input3.dat below

input3.dat
8
2.1 -1.8 -1.5
-1.7 1.6 -2.1
-1.6 -1.9 2.0
2.0 2.1 -1.6
-1.9 1.7 1.5
1.7 -1.5 2.0
2.1 2.0 1.9
-1.6 -2.0 -1.7
0.24
3.4

3. Answer question: How many times do you have to calculate the LJ potential for N particles? Typically this loop over nonbond interactions (in which the force is usually also calculated) is the most computationally expensive in molecular dynamics simulations.

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