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Merge pull request #6 from MobleyLab/lectures
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Port in lecture/instructional content from the last time I taught the corse
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@davidlmobley
davidlmobley authored Oct 26, 2017
2 parents 9849426 + d9399e5 commit 7e24776
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6 changes: 3 additions & 3 deletions uci-pharmsci/README.md
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Expand Up @@ -25,12 +25,12 @@ This will ultimately contain syllabus information, lecture notes and slides, req
- [Documentation](https://docs.eyesopen.com/toolkits/python/index.html)

- **Optionals:**
- [Atom](https://atom.io/): Github's official text editor with so many plugins.
- [Atom](https://atom.io/): GitHub's official text editor with so many plugins.
- [VIDA](https://www.eyesopen.com/vida): Molecular viewer for OEB files. (Requires OpenEye license)

#### Cheatsheets and dotfiles
Under the **uci-pharmasci/docs/** directory, I've included some useful command cheat sheets for [BASH](https://github.com/nathanmlim/blues-apps/tree/master/docs/bash_cheatsheet.jpg) and [vi](https://github.com/nathanmlim/blues-apps/tree/master/docs/vi_cheatsheet.pdf).
Under the **uci-pharmasci/docs/** directory, we have included some useful command cheat sheets for [BASH](https://github.com/nathanmlim/blues-apps/tree/master/docs/bash_cheatsheet.jpg) and [vi](https://github.com/nathanmlim/blues-apps/tree/master/docs/vi_cheatsheet.pdf).

We also have a [Github](https://www.evernote.com/shard/s26/sh/ae73a67b-4d7a-4e97-a896-cef5473db895/178762935c73b559) cheat sheet/tutorial on our group Evernote. I also recommend checking out the [CodeAcademy Github](https://www.codecademy.com/learn/learn-git) tutorial.

I've included some of my _dotfiles_ (configuration files) for VMD and Vim to set some common default settings.
We have also included several _dotfiles_ (configuration files with filenames beginning with the `.` character) for VMD and Vim to set some common default settings.
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588 changes: 588 additions & 0 deletions uci-pharmsci/lectures/3D_structure_shape/3D_Structure_Shape.ipynb
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30 changes: 30 additions & 0 deletions uci-pharmsci/lectures/3D_structure_shape/Marvin_molecule.mol
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Mrv1533004081509272D

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4,171 changes: 4,171 additions & 0 deletions uci-pharmsci/lectures/3D_structure_shape/fitted.mol2
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51 changes: 51 additions & 0 deletions uci-pharmsci/lectures/3D_structure_shape/mymolecule.mol2
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92 changes: 92 additions & 0 deletions uci-pharmsci/lectures/3D_structure_shape/ref.mol2
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396 changes: 396 additions & 0 deletions uci-pharmsci/lectures/MC_sandbox/Lec6 MC sandbox.ipynb
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430 changes: 430 additions & 0 deletions uci-pharmsci/lectures/MC_sandbox/Lec6 MC sandbox_completed.ipynb
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47 changes: 47 additions & 0 deletions uci-pharmsci/lectures/MC_sandbox/mc_sandbox.f90
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subroutine CalcEnergy(Pos, L, rc, PEnergy, Dim, NAtom)
implicit none
integer, intent(in) :: Dim, NAtom
real(8), intent(in), dimension(0:NAtom-1, 0:Dim-1) :: Pos
real(8), intent(in) :: L, rc
real(8), intent(out) :: PEnergy
real(8), parameter :: k = 3000., r0 = 1.
integer:: i, j
real(8) :: d2, sep, disp, shiftval, rc2, id6, id2, id12
real(8), dimension(Dim) :: rij, Posi


!Assign initially zeros to the force array and potential energy
PEnergy = 0.
rc2 = rc**2

!Precompute constants such as LJ shift value up here
id6 = 1./rc**6
shiftval = 4*(id6**2 - id6)


do i=0, NAtom - 1
!store Pos(i,:) in a temporary array for faster access in j looop
Posi = Pos(i,:)
do j = i+1, NAtom - 1
!compute initial rij
rij = Pos(j,:) - Posi
!Apply minimum image convention
rij = rij - L*dnint(rij / L)

!compute scalar distance
d2 = sum(rij*rij)
!Check against cutoff
if ( d2 > rc2) then
cycle
end if
id2 = 1./d2 !inverse squared distance
id6 = id2 * id2 * id2 !inverse sixth distance
id12 = id6 * id6 !inverse twelfth distance
PEnergy = Penergy + 4. * (id12 - id6) + shiftval

enddo
enddo
end subroutine


295 changes: 295 additions & 0 deletions uci-pharmsci/lectures/MD_sandbox/MD Sandbox.ipynb
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subroutine CalcEnergy(Pos, M, L, rc, PEnergy, Dim, NAtom)
implicit none
integer, intent(in) :: M, Dim, NAtom
real(8), intent(in), dimension(0:NAtom-1, 0:Dim-1) :: Pos
real(8), intent(in) :: L, rc
real(8), intent(out) :: PEnergy
real(8), parameter :: k = 3000., r0 = 1.
integer:: i, j
real(8) :: d2, sep, disp, shiftval, rc2, id6, id2, id12
real(8), dimension(Dim) :: rij, Posi


!Assign initially zeros to the force array and potential energy
PEnergy = 0.
rc2 = rc**2

!Precompute constants such as LJ shift value up here
id6 = 1./rc**6
shiftval = 4*(id6**2 - id6)


do i=0, NAtom - 1
!store Pos(i,:) in a temporary array for faster access in j looop
Posi = Pos(i,:)
do j = i+1, NAtom - 1
!compute initial rij
rij = Pos(j,:) - Posi
!Apply minimum image convention
rij = rij - L*dnint(rij / L)

!compute scalar distance
d2 = sum(rij*rij)
!Check against cutoff
if ( d2 > rc2) then
cycle
end if
id2 = 1./d2 !inverse squared distance
id6 = id2 * id2 * id2 !inverse sixth distance
id12 = id6 * id6 !inverse twelfth distance
PEnergy = Penergy + 4. * (id12 - id6) + shiftval

enddo
enddo
end subroutine



subroutine CalcEnergyForces(Pos, M, L, rc, PEnergy, Forces, Dim, NAtom)
implicit none
integer, intent(in) :: M, Dim, NAtom
real(8), intent(in), dimension(0:NAtom-1, 0:Dim-1) :: Pos
real(8), intent(in) :: L, rc
real(8), intent(out) :: PEnergy
real(8), intent(inout), dimension(0:NAtom-1, 0:Dim-1) :: Forces
!f2py intent(in, out, inplace) :: Forces
real(8), parameter :: k = 3000., r0 = 1.
integer :: i, j
real(8) :: d2, sep, disp, shiftval, rc2, id6, id2, id12
real(8), dimension(Dim) :: rij, Fij, Posi


!Assign initially zeros to the force array and potential energy
Forces = 0.
PEnergy = 0.
rc2 = rc**2

!Precompute constants such as LJ shift value up here
id6 = 1./rc**6
shiftval = 4.*(id6**2 - id6)


do i=0, NAtom - 1
!store Pos(i,:) in a temporary array for faster access in j looop
Posi = Pos(i,:)
do j = i+1, NAtom - 1
!compute initial rij
rij = Pos(j,:) - Posi
!Apply minimum image convention
rij = rij - L*dnint(rij / L)

!compute scalar distance
d2 = sum(rij*rij)
!Check against cutoff
if ( d2 > rc2) then
cycle
end if
id2 = 1./d2 !inverse squared distance
id6 = id2 * id2 * id2 !inverse sixth distance
id12 = id6 * id6 !inverse twelfth distance
PEnergy = Penergy + 4. * (id12 - id6) + shiftval
Fij = rij * (-48. * id12 + 24. * id6) * id2
Forces(i,:) = Forces(i,:) + Fij
Forces(j,:) = Forces(j,:) - Fij

enddo
enddo
end subroutine


subroutine VVIntegrate(Pos, Vel, Accel, M, L, rc, dt, KEnergy, PEnergy, Dim, NAtom)
implicit none
integer, intent(in) :: M, Dim, NAtom
real(8), intent(in) :: L, rc, dt
real(8), intent(inout), dimension(0:NAtom-1, 0:Dim-1) :: Pos, Vel, Accel
!f2py intent(in,out,inplace) :: Pos, Vel, Accel
real(8), intent(out) :: KEnergy, PEnergy
external :: CalcEnergyForces
Pos = Pos + dt * Vel + 0.5 * dt*dt * Accel
Vel = Vel + 0.5 * dt * Accel
call CalcEnergyForces(Pos, M, L, rc, PEnergy, Accel, Dim, NAtom)
Vel = Vel + 0.5 * dt * Accel
KEnergy = 0.5 * sum(Vel*Vel)
end subroutine
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