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Update fortitude version and apply --preview fixes #215

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2 changes: 1 addition & 1 deletion .github/workflows/format-lint.yml
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Expand Up @@ -30,7 +30,7 @@ jobs:
- uses: actions/checkout@v5

- name: Install fortitude linter
run: pip install fortitude-lint==0.7.1
run: pip install fortitude-lint==0.7.5

- name: Lint check
run: fortitude check src/
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2 changes: 2 additions & 0 deletions fortitude.toml
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Expand Up @@ -3,9 +3,11 @@ ignore = [
"line-too-long",
"trailing-whitespace", # we should enable this, autofix available
"incorrect-space-before-comment", # we should enable this, autofix available
"superfluous-semicolon", # same as above
"use-all", # should use "only:"
"assumed-size-character-intent", # TODO: We should fix all instances!
"implicit-external-procedures", # requires Fortran 2018
"bad-quote-string", # Use single or double quotes consistently
]
exclude = [
"src/fftw3.F90",
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1 change: 1 addition & 0 deletions ruff.toml
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@danielhollas danielhollas Oct 8, 2025

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TODO: remove this file

Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
line-length = 120
2 changes: 1 addition & 1 deletion src/compile_info.F90
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Expand Up @@ -4,7 +4,7 @@
! and the current Git commit, which is passed in from Makefile.
! allow(procedure-not-in-module) ! fortitude linter
subroutine print_compile_info()
use iso_fortran_env, only: compiler_version, compiler_options
use, intrinsic :: iso_fortran_env, only: compiler_version, compiler_options
use mod_files, only: stdout
character(len=*), parameter :: ABIN_VERSION = '1.2.0'

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4 changes: 2 additions & 2 deletions src/force_bound.F90
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Expand Up @@ -41,7 +41,7 @@ subroutine sbc_init(x, y, z)
! calculation of the cluster radius, taken from the center of mass
do iat = 1, natom
r = (x(iat, iw) - xcm)**2 + (y(iat, iw) - ycm)**2 + (z(iat, iw) - zcm)**2
r = dsqrt(r)
r = sqrt(r)
if (r > rmax .and. names(iat) /= 'H') then
rmax = r
end if
Expand Down Expand Up @@ -97,7 +97,7 @@ subroutine force_sbc(x, y, z, fx, fy, fz, walkmax)
do iw = 1, walkmax
do iat = 1, natom
r = (x(iat, iw) - xcm)**2 + (y(iat, iw) - ycm)**2 + (z(iat, iw) - zcm)**2
r = dsqrt(r)
r = sqrt(r)
if (r > rb_sbc .and. names(iat) /= 'H') then
frb = -kb_sbc * (r - rb_sbc)
fx(iat, iw) = fx(iat, iw) + frb * (x(iat, iw) - xcm) / (r)
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4 changes: 4 additions & 0 deletions src/force_h2o.F90
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Expand Up @@ -192,6 +192,8 @@ subroutine numerical_forces(x, y, z, fx, fy, fz, Epot, natom, nbeads)
y_new_forward(i, j) = y_new_forward(i, j) + DELTA
case (3)
z_new_forward(i, j) = z_new_forward(i, j) + DELTA
case default
call fatal_error(__FILE__, __LINE__, "Whoops, I should not be here!")
end select

! Calculate the energy for the forward perturbed geometry
Expand All @@ -209,6 +211,8 @@ subroutine numerical_forces(x, y, z, fx, fy, fz, Epot, natom, nbeads)
fy(i, j) = -(Epot_delta(1) - Eclas_orig) / DELTA
case (3)
fz(i, j) = -(Epot_delta(1) - Eclas_orig) / DELTA
case default
call fatal_error(__FILE__, __LINE__, "Whoops, I should not be here!")
end select
end do
end do
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6 changes: 3 additions & 3 deletions src/force_mm.F90
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Expand Up @@ -181,7 +181,7 @@ subroutine initialize_LJ(rmin, eps, num_types, natom)
if (LJcomb == 'LB') then
! WARNING: We expect rmin in angstroms!
rij = 0.5D0 * (rmin(i) + rmin(j)) * ANG
epsij = dsqrt(eps(i) * eps(j))
epsij = sqrt(eps(i) * eps(j))
end if
Bij(i, j) = 2 * 6 * epsij * rij**6
Aij(i, j) = 12 * epsij * rij**12
Expand Down Expand Up @@ -211,15 +211,15 @@ subroutine force_mm(x, y, z, fx, fy, fz, eclas, walkmax)
i = inames(iat1)
j = inames(iat2)
kLJ = ri3 * (ri3 * Aij(i, j) - Bij(i, j)) * ri
kC = q(i) * q(j) * dsqrt(ri3)
kC = q(i) * q(j) * sqrt(ri3)
fx(iat1, iw) = fx(iat1, iw) + (kLJ + kC) * dx
fx(iat2, iw) = fx(iat2, iw) - (kLJ + kC) * dx
fy(iat1, iw) = fy(iat1, iw) + (kLJ + kC) * dy
fy(iat2, iw) = fy(iat2, iw) - (kLJ + kC) * dy
fz(iat1, iw) = fz(iat1, iw) + (kLJ + kC) * dz
fz(iat2, iw) = fz(iat2, iw) - (kLJ + kC) * dz
eclas = eclas + ri3 * (ri3 * Aij(i, j) / 12 - Bij(i, j) / 6)
eclas = eclas + q(i) * q(j) / dsqrt(r)
eclas = eclas + q(i) * q(j) / sqrt(r)
end do
end do
end do
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2 changes: 1 addition & 1 deletion src/forces.F90
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Expand Up @@ -234,7 +234,7 @@ subroutine force_quantum(fx, fy, fz, x, y, z, amg, quantum_energy)
! Tuckerman normal modes Hamiltonian
! Not tested
if (inormalmodes == 2) then
ak = NWALK * TEMP**2 * amg / dsqrt(nwalk * 1.0D0)
ak = NWALK * TEMP**2 * amg / sqrt(nwalk * 1.0D0)
end if

! This is the energy coming from the Path Integral harmonic forces
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2 changes: 1 addition & 1 deletion src/geom_analysis.F90
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Expand Up @@ -33,7 +33,7 @@ subroutine print_distances(x, y, z)
! If we have only one atom, take the distance from the origin,
! i.e. [0, 0, 0]
if (natom == 1) then
r(idist) = dsqrt(x(1, iw)**2 + y(1, iw)**2 + z(1, iw)**2)
r(idist) = sqrt(x(1, iw)**2 + y(1, iw)**2 + z(1, iw)**2)
else
r(idist) = get_distance(x, y, z, dist1(idist), dist2(idist), iw)
end if
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14 changes: 7 additions & 7 deletions src/gle.F90
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Expand Up @@ -84,14 +84,14 @@ subroutine pile_init(dt, tau0)
tau = tau0 / AUtoFS * 1000
gam = 1 / tau
c1(1) = exp(-dt * gam)
c2(1) = dsqrt(1 - c1(1)**2) * dsqrt(temp * nwalk)
c2(1) = sqrt(1 - c1(1)**2) * sqrt(temp * nwalk)

! Now normal modes of bead necklace
do iw = 2, nwalk
omega = 2 * temp * nwalk * sin((iw - 1) * PI / nwalk)
gam = 2 * omega
c1(iw) = exp(-dt * gam)
c2(iw) = dsqrt(1 - c1(iw)**2) * dsqrt(temp * nwalk)
c2(iw) = sqrt(1 - c1(iw)**2) * sqrt(temp * nwalk)
end do
end subroutine pile_init

Expand All @@ -116,9 +116,9 @@ subroutine pile_step(px, py, pz, m)
! TODO: implement global version according to equations 51-54
do iw = 1, nwalk
do iat = 1, natom
px(iat, iw) = c1(iw) * px(iat, iw) + c2(iw) * ran(pom) * dsqrt(m(iat, iw))
py(iat, iw) = c1(iw) * py(iat, iw) + c2(iw) * ran(pom + 1) * dsqrt(m(iat, iw))
pz(iat, iw) = c1(iw) * pz(iat, iw) + c2(iw) * ran(pom + 2) * dsqrt(m(iat, iw))
px(iat, iw) = c1(iw) * px(iat, iw) + c2(iw) * ran(pom) * sqrt(m(iat, iw))
py(iat, iw) = c1(iw) * py(iat, iw) + c2(iw) * ran(pom + 1) * sqrt(m(iat, iw))
pz(iat, iw) = c1(iw) * pz(iat, iw) + c2(iw) * ran(pom + 2) * sqrt(m(iat, iw))
pom = pom + 3
end do
end do
Expand Down Expand Up @@ -529,7 +529,7 @@ subroutine gle_propagate(p, T, S, mass, iw)
do i = 1, ns + 1
call gautrg(ran, natom * 3)
do j = 1, natom
sqm = dsqrt(mass(j, iw))
sqm = sqrt(mass(j, iw))
p(j, i) = ran(j) * sqm
p(j + natom, i) = ran(j + natom) * sqm
p(j + natom * 2, i) = ran(j + natom * 2) * sqm
Expand Down Expand Up @@ -610,7 +610,7 @@ subroutine cholesky(SST, S, n)
end do
do i = 1, n
if (D(i, i) >= 0.0D0) then
D(i, i) = dsqrt(D(i, i))
D(i, i) = sqrt(D(i, i))
else
write (stderr, *) "WARNING: negative eigenvalue (", D(i, i), ")in LDL^T decomposition."
D(i, i) = 0.0D0
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2 changes: 2 additions & 0 deletions src/init.F90
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Expand Up @@ -762,6 +762,8 @@ subroutine print_basic_info()
write (stdout, *) ' Minimization '
case (5)
write (stdout, *) ' Landau Zener MD '
case default
call fatal_error(__FILE__, __LINE__, 'invalid ipimd in '//trim(chinput))
end select

write (stdout, *) ' using potential: '//toupper(trim(pot))
Expand Down
4 changes: 2 additions & 2 deletions src/io.F90
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Expand Up @@ -45,7 +45,7 @@ subroutine print_dipoles(dipoles, iw, nstates)
! Most QM program print Dx, Dy, Dz components first.
do ind = 1, 3 * nstates, 3
total_dip = dipoles(ind)**2 + dipoles(ind + 1)**2 + dipoles(ind + 2)**2
total_dip = dsqrt(total_dip)
total_dip = sqrt(total_dip)
write (UDIP, format2, advance="no") total_dip
end do

Expand All @@ -67,7 +67,7 @@ subroutine print_transdipoles(tdipoles, istate, ntdip)

do ind = 1, 3 * ntdip, 3
total_tdip = tdipoles(ind)**2 + tdipoles(ind + 1)**2 + tdipoles(ind + 2)**2
total_tdip = dsqrt(total_tdip)
total_tdip = sqrt(total_tdip)
write (UTDIP, format2, advance="no") total_tdip
end do

Expand Down
6 changes: 3 additions & 3 deletions src/landau_zener.F90
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Expand Up @@ -255,7 +255,7 @@ subroutine lz_hop(x, y, z, vx, vy, vz, fxc, fyc, fzc, amt, dt, eclas, chpot)
! Three point minima of adiabatic splitting Zjk
if ((en_diff(1) > en_diff(2)) .and. (en_diff(2) < en_diff(3)) .and. (it > 2)) then
second_der = ((en_diff(3) - 2 * en_diff(2) + en_diff(1)) / dt**2)
prob(ist1) = exp(-PI / 2 * (dsqrt(en_diff(2)**3 / second_der)))
prob(ist1) = exp(-PI / 2 * (sqrt(en_diff(2)**3 / second_der)))
write (fmt_in, '(I2.2)') ist
write (fmt_out, '(I2.2)') ist1
write (stdout, *) "Three-point minimum (", trim(fmt_in), "->", trim(fmt_out), &
Expand Down Expand Up @@ -364,7 +364,7 @@ subroutine lz_hop(x, y, z, vx, vy, vz, fxc, fyc, fzc, amt, dt, eclas, chpot)
call force_clas(fxc, fyc, fzc, x, y, z, eclas, pot)

!d) Simple velocity rescaling (https://doi.org/10.1063/1.4882073)
vel_rescale = dsqrt(1 - (dE / Ekin))
vel_rescale = sqrt(1 - (dE / Ekin))
do iat = 1, natom
vx(iat, 1) = vx(iat, 1) * vel_rescale
vy(iat, 1) = vy(iat, 1) * vel_rescale
Expand Down Expand Up @@ -398,7 +398,7 @@ subroutine lz_hop(x, y, z, vx, vy, vz, fxc, fyc, fzc, amt, dt, eclas, chpot)
prob = 0.0D0

Ekin = ekin_v(vx, vy, vz)
molveloc = dsqrt(2.0D0 * Ekin / sum(am(1:natom)))
molveloc = sqrt(2.0D0 * Ekin / sum(am(1:natom)))
call vranf(ran, 1)
hop_rdnum = ran(1)
icross = 0
Expand Down
32 changes: 16 additions & 16 deletions src/nosehoover.F90
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Expand Up @@ -301,9 +301,9 @@ subroutine initialize_nhc_momenta(temp)
call gautrg(ran, natom * 3)
ipom = 1
do iat = 1, natom
pnhx(iat, iw, inh) = ran(ipom) * dsqrt(temp * Qm(iw))
pnhy(iat, iw, inh) = ran(ipom + 1) * dsqrt(temp * Qm(iw))
pnhz(iat, iw, inh) = ran(ipom + 2) * dsqrt(temp * Qm(iw))
pnhx(iat, iw, inh) = ran(ipom) * sqrt(temp * Qm(iw))
pnhy(iat, iw, inh) = ran(ipom + 1) * sqrt(temp * Qm(iw))
pnhz(iat, iw, inh) = ran(ipom + 2) * sqrt(temp * Qm(iw))
end do
ipom = ipom + 3
end do
Expand All @@ -316,7 +316,7 @@ subroutine initialize_nhc_momenta(temp)
! +1 if nmolt=1, gautrg needs array at least of length=2
call gautrg(ran, nmolt + 1)
do imol = 1, nmolt
pnhx(imol, iw, inh) = ran(imol) * dsqrt(temp * ms(imol, inh))
pnhx(imol, iw, inh) = ran(imol) * sqrt(temp * ms(imol, inh))
end do
end do
end do
Expand Down Expand Up @@ -482,13 +482,13 @@ subroutine shiftNHC_yosh(px, py, pz, amt, dt)
pnhx(imol, iw, nchain) = pnhx(imol, iw, nchain) + G(nchain) * wdt2
! UPDATE THERMOSTAT VELOCITIES
do inh = 1, nchain - 1
AA = dexp(-wdt4 * pnhx(imol, iw, nchain - inh + 1) / ms(imol, nchain - inh + 1))
AA = exp(-wdt4 * pnhx(imol, iw, nchain - inh + 1) / ms(imol, nchain - inh + 1))
pnhx(imol, iw, nchain - inh) = pnhx(imol, iw, nchain - inh) * AA * AA + &
& wdt2 * G(nchain - inh) * AA
end do

! UPDATE PARTICLE VELOCITIES
AA = dexp(-wdt * pnhx(imol, iw, 1) / ms(imol, 1))
AA = exp(-wdt * pnhx(imol, iw, 1) / ms(imol, 1))
pscale = pscale * AA
! UPDATE FORCES
G(1) = pscale * pscale * ekin2 - nf * temp
Expand All @@ -501,7 +501,7 @@ subroutine shiftNHC_yosh(px, py, pz, amt, dt)

! UPDATE THERMOSTAT VELOCITIES
do inh = 1, nchain - 1
AA = dexp(-wdt4 * pnhx(imol, iw, inh + 1) / ms(imol, inh + 1))
AA = exp(-wdt4 * pnhx(imol, iw, inh + 1) / ms(imol, inh + 1))
pnhx(imol, iw, inh) = pnhx(imol, iw, inh) * AA * AA + wdt2 * G(inh) * AA
G(inh + 1) = pnhx(imol, iw, inh) * pnhx(imol, iw, inh) / ms(imol, inh) - temp
end do
Expand Down Expand Up @@ -564,23 +564,23 @@ subroutine shiftNHC_yosh_mass(px, py, pz, amt, dt)

! UPDATE THERMOSTAT VELOCITIES
do inh = 1, nchain - 1
AA = dexp(-wdt4 * pnhx(iat, iw, nchain - inh + 1) / Qm(iw))
AA = exp(-wdt4 * pnhx(iat, iw, nchain - inh + 1) / Qm(iw))
pnhx(iat, iw, nchain - inh) = pnhx(iat, iw, nchain - inh) * AA * AA + &
& wdt2 * Gx(nchain - inh) * AA
AA = dexp(-wdt4 * pnhy(iat, iw, nchain - inh + 1) / Qm(iw))
AA = exp(-wdt4 * pnhy(iat, iw, nchain - inh + 1) / Qm(iw))
pnhy(iat, iw, nchain - inh) = pnhy(iat, iw, nchain - inh) * AA * AA + &
& wdt2 * Gy(nchain - inh) * AA
AA = dexp(-wdt4 * pnhz(iat, iw, nchain - inh + 1) / Qm(iw))
AA = exp(-wdt4 * pnhz(iat, iw, nchain - inh + 1) / Qm(iw))
pnhz(iat, iw, nchain - inh) = pnhz(iat, iw, nchain - inh) * AA * AA + &
& wdt2 * Gz(nchain - inh) * AA
end do

! UPDATE PARTICLE VELOCITIES
AA = dexp(-wdt * pnhx(iat, iw, 1) / Qm(iw))
AA = exp(-wdt * pnhx(iat, iw, 1) / Qm(iw))
px(iat, iw) = px(iat, iw) * AA
AA = dexp(-wdt * pnhy(iat, iw, 1) / Qm(iw))
AA = exp(-wdt * pnhy(iat, iw, 1) / Qm(iw))
py(iat, iw) = py(iat, iw) * AA
AA = dexp(-wdt * pnhz(iat, iw, 1) / Qm(iw))
AA = exp(-wdt * pnhz(iat, iw, 1) / Qm(iw))
pz(iat, iw) = pz(iat, iw) * AA

! UPDATE FORCES
Expand All @@ -597,13 +597,13 @@ subroutine shiftNHC_yosh_mass(px, py, pz, amt, dt)

! UPDATE THERMOSTAT VELOCITIES
do inh = 1, nchain - 1
AA = dexp(-wdt4 * pnhx(iat, iw, inh + 1) / Qm(iw))
AA = exp(-wdt4 * pnhx(iat, iw, inh + 1) / Qm(iw))
pnhx(iat, iw, inh) = pnhx(iat, iw, inh) * AA * AA + wdt2 * Gx(inh) * AA
Gx(inh + 1) = pnhx(iat, iw, inh)**2 / Qm(iw) - temp
AA = dexp(-wdt4 * pnhy(iat, iw, inh + 1) / Qm(iw))
AA = exp(-wdt4 * pnhy(iat, iw, inh + 1) / Qm(iw))
pnhy(iat, iw, inh) = pnhy(iat, iw, inh) * AA * AA + wdt2 * Gy(inh) * AA
Gy(inh + 1) = pnhy(iat, iw, inh)**2 / Qm(iw) - temp
AA = dexp(-wdt4 * pnhz(iat, iw, inh + 1) / Qm(iw))
AA = exp(-wdt4 * pnhz(iat, iw, inh + 1) / Qm(iw))
pnhz(iat, iw, inh) = pnhz(iat, iw, inh) * AA * AA + wdt2 * Gz(inh) * AA
Gz(inh + 1) = pnhz(iat, iw, inh)**2 / Qm(iw) - temp
end do
Expand Down
2 changes: 1 addition & 1 deletion src/plumed.F90
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Expand Up @@ -5,7 +5,7 @@
! PLUMED is statically linked with ABIN, see Makefile.
! To install PLUMED libraries, see 'dev_scripts/install_plumed.sh'
module mod_plumed
use iso_c_binding, only: C_NULL_PTR
use, intrinsic :: iso_c_binding, only: C_NULL_PTR
use mod_const, only: DP
#ifndef USE_PLUMED
use mod_error, only: not_compiled_with
Expand Down
10 changes: 5 additions & 5 deletions src/potentials.F90
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Expand Up @@ -231,7 +231,7 @@ subroutine force_harmonic_rotor(x, y, z, fx, fy, fz, eclas, nwalk)
dy = y(2, i) - y(1, i)
dz = z(2, i) - z(1, i)
r = dx**2 + dy**2 + dz**2
r = dsqrt(r)
r = sqrt(r)
fac = hrot%k * (r - hrot%r0) / r
fx(1, i) = fac * dx
fx(2, i) = -fx(1, i)
Expand All @@ -258,7 +258,7 @@ subroutine hessian_harmonic_rotor(x, y, z, nwalk, hess)
dy = y(2, i) - y(1, i)
dz = z(2, i) - z(1, i)
r = dx**2 + dy**2 + dz**2
r = dsqrt(r)
r = sqrt(r)
fac = hrot%k * (r - hrot%r0) / r
hess(1, 1, i) = (hrot%k * dx**2 / r**2 - fac * dx**2 / r**2 + fac) / nwalk
hess(2, 2, i) = (hrot%k * dy**2 / r**2 - fac * dy**2 / r**2 + fac) / nwalk
Expand Down Expand Up @@ -313,7 +313,7 @@ subroutine morse_init(natom, k_morse, r0, d0)
call real_positive(d0, 'd0_morse')
call real_positive(r0, 'r0_morse')

a = dsqrt(k_morse / 2.0D0 / d0)
a = sqrt(k_morse / 2.0D0 / d0)
morse = morse_params(d0=d0, a=a, r0=r0)
end subroutine morse_init

Expand All @@ -332,7 +332,7 @@ subroutine force_morse(x, y, z, fx, fy, fz, eclas, nwalk)
dy = y(2, i) - y(1, i)
dz = z(2, i) - z(1, i)
r = dx**2 + dy**2 + dz**2
r = dsqrt(r)
r = sqrt(r)
ex = exp(-morse%a * (r - morse%r0))
fac = 2 * morse%a * ex * morse%d0 * (1 - ex) / r
fx(1, i) = fac * dx
Expand Down Expand Up @@ -364,7 +364,7 @@ subroutine hessian_morse(x, y, z, nwalk, hess)
dy = y(2, i) - y(1, i)
dz = z(2, i) - z(1, i)
r = dx**2 + dy**2 + dz**2
r = dsqrt(r)
r = sqrt(r)
ex = exp(-a * (r - morse%r0))
fac = 2 * a * ex * morse%d0 * (1 - ex) / r
fac2 = 2 * morse%d0 * a**2 * ex**2 / r**2
Expand Down
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