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Remove non-UTF-8 characters in Fortran modules #203

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Remove non-UTF-8 characters in Fortran modules #203

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e566c93
Remove non-UTF-8 characters in Fortran modules
mortele Jan 26, 2023
02c8b24
Pin Jinja2 version to <3.1 to fix sphinx ImportError
mortele Jan 26, 2023
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1 change: 1 addition & 0 deletions docs/docs_requirements.txt
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Expand Up @@ -6,3 +6,4 @@ sphinxcontrib.bibtex
matplotlib
numpy
numpydoc
Jinja2<3.1
2 changes: 1 addition & 1 deletion hymd/compute_angle_forces.f90
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Expand Up @@ -74,7 +74,7 @@ subroutine caf(f, r, box, a, b, c, t0, k, energy)

xrasin = -ff / (norm_a * sinphi)
xrcsin = -ff / (norm_c * sinphi)
! 𝜕θ/𝜕cos(θ) * 𝜕cos(θ)/𝜕r
! d theta / d cos(theta) * d cos(theta) / dr
fa = (ec - cosphi * ea) * xrasin
fc = (ea - cosphi * ec) * xrcsin

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2 changes: 1 addition & 1 deletion hymd/compute_angle_forces__double.f90
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Expand Up @@ -74,7 +74,7 @@ subroutine caf_d(f, r, box, a, b, c, t0, k, energy)

xrasin = -ff / (norm_a * sinphi)
xrcsin = -ff / (norm_c * sinphi)
! 𝜕θ/𝜕cos(θ) * 𝜕cos(θ)/𝜕r
! d theta / d cos(theta) * d cos(theta) / dr
fa = (ec - cosphi * ea) * xrasin
fc = (ea - cosphi * ec) * xrcsin

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16 changes: 8 additions & 8 deletions hymd/dipole_reconstruction.f90
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Expand Up @@ -111,13 +111,13 @@ subroutine reconstruct(rab, rb, rcb, box, c_k, d_k, phi, dipole_flag, energy_cbt

if (sin_gamma < 0.1) then
print *, "DIHEDRAL ROUTINE WARNING (bending potential):"
print '(a, f5.2, a)', "The angle γ =", gamm, " is too close to 0 or π."
print *, "There's probably something wrong with the simulation. Setting sin(γ) = 0.1"
print '(a, f5.2, a)', "The angle gamma =", gamm, " is too close to 0 or pi."
print *, "There's probably something wrong with the simulation. Setting sin(gamma) = 0.1"
sin_gamma = 0.1
end if

! Bending "forces" == f_gamma_i in the paper
! 1/sin(γ) ∂cos(γ)/∂γ
! 1 / sin(gamma) d cos(gamma) / d gamma
fa = (v - cos_gamma * w) / norm_a
fc = (w - cos_gamma * v) / norm_c

Expand All @@ -143,7 +143,7 @@ subroutine reconstruct(rab, rb, rcb, box, c_k, d_k, phi, dipole_flag, energy_cbt
end if

! 2 - Dipole reconstruction
! θ(γ)
! theta(gamma)
! This function needs to be fit again
fac = exp((gamm - 1.73d0) / 0.025d0)
theta = -1.607d0 * gamm + 0.094d0 + 1.883d0 / (1.d0 + fac)
Expand Down Expand Up @@ -186,7 +186,7 @@ subroutine reconstruct(rab, rb, rcb, box, c_k, d_k, phi, dipole_flag, energy_cbt

! Last term is 0 for N_a, second term is 0 for N_c (S19)
! Minus in the last term because inverse cross_matrix
! 1 / sin(γ) is already inside fa, fb, and fc
! 1 / sin(gamma) is already inside fa, fb, and fc
N_a = (cos_gamma * outer_product(fa, n) + cross_matrix(W_a, v) ) / sin_gamma
N_b = (cos_gamma * outer_product(fb, n) + cross_matrix(W_b, v) - cross_matrix(V_b, w)) / sin_gamma
N_c = (cos_gamma * outer_product(fc, n) - cross_matrix(V_c, w)) / sin_gamma
Expand All @@ -195,9 +195,9 @@ subroutine reconstruct(rab, rb, rcb, box, c_k, d_k, phi, dipole_flag, energy_cbt
M_b = cross_matrix(N_b, v) - cross_matrix(V_b, n)
M_c = cross_matrix(N_c, v) - cross_matrix(V_c, n)

! A lot of terms in (S10) go away because ∂φ/∂γ = 0,
! since φ = const.
! 1 / sin(γ) is already inside fa, fb, and fc
! A lot of terms in (S10) go away because d phi / d gamma = 0,
! since phi = const.
! 1 / sin(gamma) is already inside fa, fb, and fc
FN_a = sin_theta * d_theta * outer_product(fa, n)
FN_b = sin_theta * d_theta * outer_product(fb, n)
FN_c = sin_theta * d_theta * outer_product(fc, n)
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16 changes: 8 additions & 8 deletions hymd/dipole_reconstruction__double.f90
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Original file line number Diff line number Diff line change
Expand Up @@ -111,13 +111,13 @@ subroutine reconstruct(rab, rb, rcb, box, c_k, d_k, phi, dipole_flag, energy_cbt

if (sin_gamma < 0.1) then
print *, "DIHEDRAL ROUTINE WARNING (bending potential):"
print '(a, f5.2, a)', "The angle γ =", gamm, " is too close to 0 or π."
print *, "There's probably something wrong with the simulation. Setting sin(γ) = 0.1"
print '(a, f5.2, a)', "The angle gamma =", gamm, " is too close to 0 or pi."
print *, "There's probably something wrong with the simulation. Setting sin(gamma) = 0.1"
sin_gamma = 0.1
end if

! Bending "forces" == f_gamma_i in the paper
! 1/sin(γ) ∂cos(γ)/∂γ
! 1 / sin(gamma) d cos(gamma) / d gamma
fa = (v - cos_gamma * w) / norm_a
fc = (w - cos_gamma * v) / norm_c

Expand All @@ -143,7 +143,7 @@ subroutine reconstruct(rab, rb, rcb, box, c_k, d_k, phi, dipole_flag, energy_cbt
end if

! 2 - Dipole reconstruction
! θ(γ)
! theta(gamma)
! This function needs to be fit again
fac = exp((gamm - 1.73d0) / 0.025d0)
theta = -1.607d0 * gamm + 0.094d0 + 1.883d0 / (1.d0 + fac)
Expand Down Expand Up @@ -186,7 +186,7 @@ subroutine reconstruct(rab, rb, rcb, box, c_k, d_k, phi, dipole_flag, energy_cbt

! Last term is 0 for N_a, second term is 0 for N_c (S19)
! Minus in the last term because inverse cross_matrix
! 1 / sin(γ) is already inside fa, fb, and fc
! 1 / sin(gamma) is already inside fa, fb, and fc
N_a = (cos_gamma * outer_product(fa, n) + cross_matrix(W_a, v) ) / sin_gamma
N_b = (cos_gamma * outer_product(fb, n) + cross_matrix(W_b, v) - cross_matrix(V_b, w)) / sin_gamma
N_c = (cos_gamma * outer_product(fc, n) - cross_matrix(V_c, w)) / sin_gamma
Expand All @@ -195,9 +195,9 @@ subroutine reconstruct(rab, rb, rcb, box, c_k, d_k, phi, dipole_flag, energy_cbt
M_b = cross_matrix(N_b, v) - cross_matrix(V_b, n)
M_c = cross_matrix(N_c, v) - cross_matrix(V_c, n)

! A lot of terms in (S10) go away because ∂φ/∂γ = 0,
! since φ = const.
! 1 / sin(γ) is already inside fa, fb, and fc
! A lot of terms in (S10) go away because d phi / d gamma = 0,
! since phi = const.
! 1 / sin(gamma) is already inside fa, fb, and fc
FN_a = sin_theta * d_theta * outer_product(fa, n)
FN_b = sin_theta * d_theta * outer_product(fb, n)
FN_c = sin_theta * d_theta * outer_product(fc, n)
Expand Down