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@ -6,9 +6,10 @@
#+LATEX_CLASS: report #+LATEX_CLASS: report
#+LATEX_HEADER_EXTRA: \usepackage{minted} #+LATEX_HEADER_EXTRA: \usepackage{minted}
#+HTML_HEAD: <link rel="stylesheet" title="Standard" href="worg.css" type="text/css" /> #+HTML_HEAD: <link rel="stylesheet" title="Standard" href="worg.css" type="text/css" />
#+OPTIONS: H:2 num:t toc:nil \n:nil @:t ::t |:t ^:t -:t f:t *:t <:t #+OPTIONS: H:4 num:t toc:t \n:nil @:t ::t |:t ^:t -:t f:t *:t <:t
#+OPTIONS: TeX:t LaTeX:t skip:nil d:nil todo:t pri:nil tags:not-in-toc #+OPTIONS: TeX:t LaTeX:t skip:nil d:nil todo:t pri:nil tags:not-in-toc
#+EXPORT_EXCLUDE_TAGS: solution # EXCLUDE_TAGS: Python solution
# EXCLUDE_TAGS: Fortran solution
#+BEGIN_SRC elisp :output none :exports none #+BEGIN_SRC elisp :output none :exports none
(setq org-latex-listings 'minted (setq org-latex-listings 'minted
@ -54,7 +55,7 @@
*Note* *Note*
#+begin_important #+begin_important
In Fortran, when you use a double precision constant, don't forget In Fortran, when you use a double precision constant, don't forget
to put d0 as a suffix (for example 2.0d0), or it will be to put ~d0~ as a suffix (for example ~2.0d0~), or it will be
interpreted as a single precision value interpreted as a single precision value
#+end_important #+end_important
@ -68,32 +69,31 @@
\Psi(\mathbf{r}) = \exp(-a |\mathbf{r}|) \Psi(\mathbf{r}) = \exp(-a |\mathbf{r}|)
$$ $$
We will first verify that $\Psi$ is an eigenfunction of the Hamiltonian We will first verify that, for a given value of $a$, $\Psi$ is an
eigenfunction of the Hamiltonian
$$ $$
\hat{H} = \hat{T} + \hat{V} = - \frac{1}{2} \Delta - \frac{1}{|\mathbf{r}|} \hat{H} = \hat{T} + \hat{V} = - \frac{1}{2} \Delta - \frac{1}{|\mathbf{r}|}
$$ $$
when $a=1$, by checking that $\hat{H}\Psi(\mathbf{r}) = E\Psi(\mathbf{r})$ for To do that, we will check if the local energy, defined as
all $\mathbf{r}$. We will check that the local energy, defined as
$$ $$
E_L(\mathbf{r}) = \frac{\hat{H} \Psi(\mathbf{r})}{\Psi(\mathbf{r})}, E_L(\mathbf{r}) = \frac{\hat{H} \Psi(\mathbf{r})}{\Psi(\mathbf{r})},
$$ $$
is constant. We will also see that when $a \ne 1$ the local energy is constant.
is not constant, so $\hat{H} \Psi \ne E \Psi$.
The probabilistic /expected value/ of an arbitrary function $f(x)$ The probabilistic /expected value/ of an arbitrary function $f(x)$
with respect to a probability density function $p(x)$ is given by with respect to a probability density function $p(x)$ is given by
$$ \langle f \rangle_p = \int_{-\infty}^\infty p(x)\, f(x)\,dx $$. $$ \langle f \rangle_p = \int_{-\infty}^\infty p(x)\, f(x)\,dx. $$
Recall that a probability density function $p(x)$ is non-negative Recall that a probability density function $p(x)$ is non-negative
and integrates to one: and integrates to one:
$$ \int_{-\infty}^\infty p(x)\,dx = 1 $$. $$ \int_{-\infty}^\infty p(x)\,dx = 1. $$
The electronic energy of a system is the expectation value of the The electronic energy of a system is the expectation value of the
@ -114,8 +114,18 @@
:header-args:f90: :tangle hydrogen.f90 :header-args:f90: :tangle hydrogen.f90
:END: :END:
Write all the functions of this section in a single file :
~hydrogen.py~ if you use Python, or ~hydrogen.f90~ is you use
Fortran.
*** Exercise 1 *** Exercise 1
#+begin_exercise
Find the theoretical value of $a$ for which $\Psi$ is an eigenfunction of $\hat{H}$.
#+end_exercise
*** Exercise 2
#+begin_exercise #+begin_exercise
Write a function which computes the potential at $\mathbf{r}$. Write a function which computes the potential at $\mathbf{r}$.
The function accepts a 3-dimensional vector =r= as input arguments The function accepts a 3-dimensional vector =r= as input arguments
@ -127,7 +137,15 @@
V(\mathbf{r}) = -\frac{1}{\sqrt{x^2 + y^2 + z^2}} V(\mathbf{r}) = -\frac{1}{\sqrt{x^2 + y^2 + z^2}}
$$ $$
*Python* **** Python
#+BEGIN_SRC python :results none :tangle none
import numpy as np
def potential(r):
# TODO
#+END_SRC
**** Python :solution:
#+BEGIN_SRC python :results none #+BEGIN_SRC python :results none
import numpy as np import numpy as np
@ -135,8 +153,16 @@ def potential(r):
return -1. / np.sqrt(np.dot(r,r)) return -1. / np.sqrt(np.dot(r,r))
#+END_SRC #+END_SRC
**** Fortran
#+BEGIN_SRC f90 :tangle none
double precision function potential(r)
implicit none
double precision, intent(in) :: r(3)
! TODO
end function potential
#+END_SRC
*Fortran* **** Fortran :solution:
#+BEGIN_SRC f90 #+BEGIN_SRC f90
double precision function potential(r) double precision function potential(r)
implicit none implicit none
@ -145,7 +171,7 @@ double precision function potential(r)
end function potential end function potential
#+END_SRC #+END_SRC
*** Exercise 2 *** Exercise 3
#+begin_exercise #+begin_exercise
Write a function which computes the wave function at $\mathbf{r}$. Write a function which computes the wave function at $\mathbf{r}$.
The function accepts a scalar =a= and a 3-dimensional vector =r= as The function accepts a scalar =a= and a 3-dimensional vector =r= as
@ -153,13 +179,28 @@ end function potential
#+end_exercise #+end_exercise
*Python* **** Python
#+BEGIN_SRC python :results none
def psi(a, r):
# TODO
#+END_SRC
**** Python :solution:
#+BEGIN_SRC python :results none #+BEGIN_SRC python :results none
def psi(a, r): def psi(a, r):
return np.exp(-a*np.sqrt(np.dot(r,r))) return np.exp(-a*np.sqrt(np.dot(r,r)))
#+END_SRC #+END_SRC
*Fortran* **** Fortran
#+BEGIN_SRC f90
double precision function psi(a, r)
implicit none
double precision, intent(in) :: a, r(3)
! TODO
end function psi
#+END_SRC
**** Fortran :solution:
#+BEGIN_SRC f90 #+BEGIN_SRC f90
double precision function psi(a, r) double precision function psi(a, r)
implicit none implicit none
@ -168,7 +209,7 @@ double precision function psi(a, r)
end function psi end function psi
#+END_SRC #+END_SRC
*** Exercise 3 *** Exercise 4
#+begin_exercise #+begin_exercise
Write a function which computes the local kinetic energy at $\mathbf{r}$. Write a function which computes the local kinetic energy at $\mathbf{r}$.
The function accepts =a= and =r= as input arguments and returns the The function accepts =a= and =r= as input arguments and returns the
@ -205,13 +246,28 @@ end function psi
-\frac{1}{2} \frac{\Delta \Psi}{\Psi} (\mathbf{r}) = -\frac{1}{2}\left(a^2 - \frac{2a}{\mathbf{|r|}} \right) -\frac{1}{2} \frac{\Delta \Psi}{\Psi} (\mathbf{r}) = -\frac{1}{2}\left(a^2 - \frac{2a}{\mathbf{|r|}} \right)
$$ $$
*Python* **** Python
#+BEGIN_SRC python :results none
def kinetic(a,r):
# TODO
#+END_SRC
**** Python :solution:
#+BEGIN_SRC python :results none #+BEGIN_SRC python :results none
def kinetic(a,r): def kinetic(a,r):
return -0.5 * (a**2 - (2.*a)/np.sqrt(np.dot(r,r))) return -0.5 * (a**2 - (2.*a)/np.sqrt(np.dot(r,r)))
#+END_SRC #+END_SRC
*Fortran* **** Fortran
#+BEGIN_SRC f90
double precision function kinetic(a,r)
implicit none
double precision, intent(in) :: a, r(3)
! TODO
end function kinetic
#+END_SRC
**** Fortran :solution:
#+BEGIN_SRC f90 #+BEGIN_SRC f90
double precision function kinetic(a,r) double precision function kinetic(a,r)
implicit none implicit none
@ -221,11 +277,12 @@ double precision function kinetic(a,r)
end function kinetic end function kinetic
#+END_SRC #+END_SRC
*** Exercise 4 *** Exercise 5
#+begin_exercise #+begin_exercise
Write a function which computes the local energy at $\mathbf{r}$. Write a function which computes the local energy at $\mathbf{r}$,
The function accepts =x,y,z= as input arguments and returns the using the previously defined functions.
local energy. The function accepts =a= and =r= as input arguments and returns the
local kinetic energy.
#+end_exercise #+end_exercise
$$ $$
@ -233,13 +290,28 @@ end function kinetic
$$ $$
*Python* **** Python
#+BEGIN_SRC python :results none
def e_loc(a,r):
#TODO
#+END_SRC
**** Python :solution:
#+BEGIN_SRC python :results none #+BEGIN_SRC python :results none
def e_loc(a,r): def e_loc(a,r):
return kinetic(a,r) + potential(r) return kinetic(a,r) + potential(r)
#+END_SRC #+END_SRC
*Fortran* **** Fortran
#+BEGIN_SRC f90
double precision function e_loc(a,r)
implicit none
double precision, intent(in) :: a, r(3)
! TODO
end function e_loc
#+END_SRC
**** Fortran :solution:
#+BEGIN_SRC f90 #+BEGIN_SRC f90
double precision function e_loc(a,r) double precision function e_loc(a,r)
implicit none implicit none
@ -254,47 +326,98 @@ end function e_loc
:header-args:python: :tangle plot_hydrogen.py :header-args:python: :tangle plot_hydrogen.py
:header-args:f90: :tangle plot_hydrogen.f90 :header-args:f90: :tangle plot_hydrogen.f90
:END: :END:
*** Exercise *** Exercise
#+begin_exercise #+begin_exercise
For multiple values of $a$ (0.1, 0.2, 0.5, 1., 1.5, 2.), plot the For multiple values of $a$ (0.1, 0.2, 0.5, 1., 1.5, 2.), plot the
local energy along the $x$ axis. local energy along the $x$ axis. In Python, you can use matplotlib
for example. In Fortran, it is convenient to write in a text file
the values of $x$ and $E_L(\mathbf{r})$ for each point, and use
Gnuplot to plot the files.
#+end_exercise #+end_exercise
*Python* **** Python
#+BEGIN_SRC python :results none #+BEGIN_SRC python :results none
import numpy as np import numpy as np
import matplotlib.pyplot as plt import matplotlib.pyplot as plt
from hydrogen import e_loc from hydrogen import e_loc
x=np.linspace(-5,5) x=np.linspace(-5,5)
def make_array(a):
y=np.array([ e_loc(a, np.array([t,0.,0.]) ) for t in x])
return y
plt.figure(figsize=(10,5)) plt.figure(figsize=(10,5))
# TODO
plt.tight_layout()
plt.legend()
plt.savefig("plot_py.png")
#+end_src
**** Python :solution:
#+BEGIN_SRC python :results none
import numpy as np
import matplotlib.pyplot as plt
from hydrogen import e_loc
x=np.linspace(-5,5)
plt.figure(figsize=(10,5))
for a in [0.1, 0.2, 0.5, 1., 1.5, 2.]: for a in [0.1, 0.2, 0.5, 1., 1.5, 2.]:
y = make_array(a) y=np.array([ e_loc(a, np.array([t,0.,0.]) ) for t in x])
plt.plot(x,y,label=f"a={a}") plt.plot(x,y,label=f"a={a}")
plt.tight_layout() plt.tight_layout()
plt.legend() plt.legend()
plt.savefig("plot_py.png") plt.savefig("plot_py.png")
#+end_src #+end_src
#+RESULTS: #+RESULTS:
[[./plot_py.png]] [[./plot_py.png]]
**** Fortran
#+begin_src f90
program plot
implicit none
double precision, external :: e_loc
double precision :: x(50), dx
*Fortran* integer :: i, j
#+begin_src f90
dx = 10.d0/(size(x)-1)
do i=1,size(x)
x(i) = -5.d0 + (i-1)*dx
end do
! TODO
end program plot
#+end_src
To compile and run:
#+begin_src sh :exports both
gfortran hydrogen.f90 plot_hydrogen.f90 -o plot_hydrogen
./plot_hydrogen > data
#+end_src
To plot the data using gnuplot:
#+begin_src gnuplot :file plot.png :exports both
set grid
set xrange [-5:5]
set yrange [-2:1]
plot './data' index 0 using 1:2 with lines title 'a=0.1', \
'./data' index 1 using 1:2 with lines title 'a=0.2', \
'./data' index 2 using 1:2 with lines title 'a=0.5', \
'./data' index 3 using 1:2 with lines title 'a=1.0', \
'./data' index 4 using 1:2 with lines title 'a=1.5', \
'./data' index 5 using 1:2 with lines title 'a=2.0'
#+end_src
**** Fortran :solution:
#+begin_src f90
program plot program plot
implicit none implicit none
double precision, external :: e_loc double precision, external :: e_loc
@ -323,20 +446,20 @@ program plot
end do end do
end program plot end program plot
#+end_src #+end_src
To compile and run: To compile and run:
#+begin_src sh :exports both #+begin_src sh :exports both
gfortran hydrogen.f90 plot_hydrogen.f90 -o plot_hydrogen gfortran hydrogen.f90 plot_hydrogen.f90 -o plot_hydrogen
./plot_hydrogen > data ./plot_hydrogen > data
#+end_src #+end_src
#+RESULTS: #+RESULTS:
To plot the data using gnuplot: To plot the data using gnuplot:
#+begin_src gnuplot :file plot.png :exports both #+begin_src gnuplot :file plot.png :exports both
set grid set grid
set xrange [-5:5] set xrange [-5:5]
set yrange [-2:1] set yrange [-2:1]
@ -346,12 +469,12 @@ plot './data' index 0 using 1:2 with lines title 'a=0.1', \
'./data' index 3 using 1:2 with lines title 'a=1.0', \ './data' index 3 using 1:2 with lines title 'a=1.0', \
'./data' index 4 using 1:2 with lines title 'a=1.5', \ './data' index 4 using 1:2 with lines title 'a=1.5', \
'./data' index 5 using 1:2 with lines title 'a=2.0' './data' index 5 using 1:2 with lines title 'a=2.0'
#+end_src #+end_src
#+RESULTS: #+RESULTS:
[[file:plot.png]] [[file:plot.png]]
** Numerical estimation of the energy ** TODO Numerical estimation of the energy
:PROPERTIES: :PROPERTIES:
:header-args:python: :tangle energy_hydrogen.py :header-args:python: :tangle energy_hydrogen.py
:header-args:f90: :tangle energy_hydrogen.f90 :header-args:f90: :tangle energy_hydrogen.f90
@ -476,7 +599,7 @@ gfortran hydrogen.f90 energy_hydrogen.f90 -o energy_hydrogen
: a = 1.5000000000000000 E = -0.39242967082602065 : a = 1.5000000000000000 E = -0.39242967082602065
: a = 2.0000000000000000 E = -8.0869806678448772E-002 : a = 2.0000000000000000 E = -8.0869806678448772E-002
** Variance of the local energy ** TODO Variance of the local energy
:PROPERTIES: :PROPERTIES:
:header-args:python: :tangle variance_hydrogen.py :header-args:python: :tangle variance_hydrogen.py
:header-args:f90: :tangle variance_hydrogen.f90 :header-args:f90: :tangle variance_hydrogen.f90
@ -618,7 +741,7 @@ gfortran hydrogen.f90 variance_hydrogen.f90 -o variance_hydrogen
: a = 2.0000000000000000 E = -8.0869806678448772E-002 s2 = 1.8068814270846534 : a = 2.0000000000000000 E = -8.0869806678448772E-002 s2 = 1.8068814270846534
* Variational Monte Carlo * TODO Variational Monte Carlo
Numerical integration with deterministic methods is very efficient Numerical integration with deterministic methods is very efficient
in low dimensions. When the number of dimensions becomes large, in low dimensions. When the number of dimensions becomes large,
@ -629,7 +752,7 @@ gfortran hydrogen.f90 variance_hydrogen.f90 -o variance_hydrogen
to the discretization of space, and compute a statistical confidence to the discretization of space, and compute a statistical confidence
interval. interval.
** Computation of the statistical error ** TODO Computation of the statistical error
:PROPERTIES: :PROPERTIES:
:header-args:python: :tangle qmc_stats.py :header-args:python: :tangle qmc_stats.py
:header-args:f90: :tangle qmc_stats.f90 :header-args:f90: :tangle qmc_stats.f90
@ -694,7 +817,7 @@ subroutine ave_error(x,n,ave,err)
end subroutine ave_error end subroutine ave_error
#+END_SRC #+END_SRC
** Uniform sampling in the box ** TODO Uniform sampling in the box
:PROPERTIES: :PROPERTIES:
:header-args:python: :tangle qmc_uniform.py :header-args:python: :tangle qmc_uniform.py
:header-args:f90: :tangle qmc_uniform.f90 :header-args:f90: :tangle qmc_uniform.f90
@ -816,7 +939,7 @@ gfortran hydrogen.f90 qmc_stats.f90 qmc_uniform.f90 -o qmc_uniform
#+RESULTS: #+RESULTS:
: E = -0.49588321986667677 +/- 7.1758863546737969E-004 : E = -0.49588321986667677 +/- 7.1758863546737969E-004
** Metropolis sampling with $\Psi^2$ ** TODO Metropolis sampling with $\Psi^2$
:PROPERTIES: :PROPERTIES:
:header-args:python: :tangle qmc_metropolis.py :header-args:python: :tangle qmc_metropolis.py
:header-args:f90: :tangle qmc_metropolis.f90 :header-args:f90: :tangle qmc_metropolis.f90
@ -1000,7 +1123,7 @@ gfortran hydrogen.f90 qmc_stats.f90 qmc_metropolis.f90 -o qmc_metropolis
: E = -0.49478505004797046 +/- 2.0493795299184956E-004 : E = -0.49478505004797046 +/- 2.0493795299184956E-004
: A = 0.51737800000000000 +/- 4.1827406733181444E-004 : A = 0.51737800000000000 +/- 4.1827406733181444E-004
** Gaussian random number generator ** TODO Gaussian random number generator
To obtain Gaussian-distributed random numbers, you can apply the To obtain Gaussian-distributed random numbers, you can apply the
[[https://en.wikipedia.org/wiki/Box%E2%80%93Muller_transform][Box Muller transform]] to uniform random numbers: [[https://en.wikipedia.org/wiki/Box%E2%80%93Muller_transform][Box Muller transform]] to uniform random numbers:
@ -1045,7 +1168,7 @@ subroutine random_gauss(z,n)
end subroutine random_gauss end subroutine random_gauss
#+END_SRC #+END_SRC
** Generalized Metropolis algorithm ** TODO Generalized Metropolis algorithm
:PROPERTIES: :PROPERTIES:
:header-args:python: :tangle vmc_metropolis.py :header-args:python: :tangle vmc_metropolis.py
:header-args:f90: :tangle vmc_metropolis.f90 :header-args:f90: :tangle vmc_metropolis.f90
@ -1290,9 +1413,9 @@ gfortran hydrogen.f90 qmc_stats.f90 vmc_metropolis.f90 -o vmc_metropolis
:header-args:f90: :tangle dmc.f90 :header-args:f90: :tangle dmc.f90
:END: :END:
** Hydrogen atom ** TODO Hydrogen atom
**** Exercise *** Exercise
#+begin_exercise #+begin_exercise
Modify the Metropolis VMC program to introduce the PDMC weight. Modify the Metropolis VMC program to introduce the PDMC weight.
@ -1439,7 +1562,7 @@ gfortran hydrogen.f90 qmc_stats.f90 vmc_metropolis.f90 -o vmc_metropolis
: A = 0.78861366666666655 +/- 3.5096729498002445E-004 : A = 0.78861366666666655 +/- 3.5096729498002445E-004
** Dihydrogen ** TODO Dihydrogen
We will now consider the H_2 molecule in a minimal basis composed of the We will now consider the H_2 molecule in a minimal basis composed of the
$1s$ orbitals of the hydrogen atoms: $1s$ orbitals of the hydrogen atoms: