Fix clang-format errors

Author: ahojukka5

.clang-format

@@ -8,7 +8,7 @@
 IndentWidth: 2
 TabWidth: 2
 UseTab: Never
-ColumnLimit: 100
+ColumnLimit: 80
 
 # Allow things on a single line
 
@@ -18,11 +18,14 @@ AllowShortFunctionsOnASingleLine: All
 AllowShortLambdasOnASingleLine: true
 AllowShortCaseLabelsOnASingleLine: true
 
+# List styles: { a, b, c } or {a, b, c} ?
+# Cpp11BracedListStyle: false
+
 # Constructor formatting
 
 # ensures that : is placed on a new line
 BreakConstructorInitializers: BeforeColon
 ConstructorInitializerAllOnOneLineOrOnePerLine: false # puts each initializer on its own line
 AllowAllConstructorInitializersOnNextLine: false # disables grouping on the next line
-BinPackParameters: false # prevents squeezing multiple parameters into one line
+BinPackParameters: true # prevents squeezing multiple parameters into one line
 AlignAfterOpenBracket: Align # keeps nice vertical alignment

apps/aluminumNew/Aluminum.hpp

@@ -11,15 +11,17 @@ using namespace pfc;
 using namespace pfc::ui;
 
 /**
- * @brief Aluminum model class for OpenPFC. This class is used to define the model.
+ * @brief Aluminum model class for OpenPFC. This class is used to define the
+ * model.
  *
  */
 class Aluminum : public Model {
 
 private:
   std::vector<double> filterMF, opL, opN, opEps, P_F;
   std::vector<double> psiMF, psi, psiN, P_star_psi, temperature, stress;
-  std::vector<std::complex<double>> psiMF_F, psi_F, psiN_F, P_psi_F, temperature_F, stress_F;
+  std::vector<std::complex<double>> psiMF_F, psi_F, psiN_F, P_psi_F,
+      temperature_F, stress_F;
   size_t mem_allocated = 0;
   bool m_first = true;
 
@@ -78,8 +80,12 @@ class Aluminum : public Model {
   void set_x_initial(double x_initial) { params.x_initial = x_initial; }
   void set_m_xpos(double m_xpos) { params.m_xpos = m_xpos; }
   void set_alpha(double alpha) { params.alpha = alpha; }
-  void set_alpha_farTol(double alpha_farTol) { params.alpha_farTol = alpha_farTol; }
-  void set_alpha_highOrd(int alpha_highOrd) { params.alpha_highOrd = alpha_highOrd; }
+  void set_alpha_farTol(double alpha_farTol) {
+    params.alpha_farTol = alpha_farTol;
+  }
+  void set_alpha_highOrd(int alpha_highOrd) {
+    params.alpha_highOrd = alpha_highOrd;
+  }
   void set_tau_const(double tau_const) { params.tau_const = tau_const; }
   void set_lambda(double lambda) { params.lambda = lambda; }
   void set_stabP(double stabP) { params.stabP = stabP; }
@@ -207,7 +213,8 @@ class Aluminum : public Model {
 
           P_F[idx] = params.Bx * exp(-params.tau_const) * peak;
 
-          double opCk = params.stabP + params.p2_bar - P_F[idx] + params.q2_bar_L * fMF;
+          double opCk =
+              params.stabP + params.p2_bar - P_F[idx] + params.q2_bar_L * fMF;
 
           filterMF[idx] = fMF;
           opL[idx] = exp(kLap * opCk * dt);
@@ -267,18 +274,26 @@ class Aluminum : public Model {
         for (int i = low[0]; i <= high[0]; i++) {
           double x = x0 + i * dx;
           double dist = x + fullruns - (x > steppoint) * l;
-          double T_var = params.G_grid * (dist - params.x_initial - params.V_grid * t);
+          double T_var =
+              params.G_grid * (dist - params.x_initial - params.V_grid * t);
           temperature[idx] = T_var;
           double q2_bar_N = params.q21_bar * T_var / params.T0;
-          double q3_bar = params.q31_bar * (params.T_const + T_var) / params.T0 + params.q30_bar;
+          double q3_bar =
+              params.q31_bar * (params.T_const + T_var) / params.T0 +
+              params.q30_bar;
           double u = psi[idx];
           double v = psiMF[idx];
-          double kernel_term_N = -(1.0 - exp(-T_var / params.T0)) * P_star_psi[idx];
-          psiN[idx] = params.p3_bar * u * u + params.p4_bar * u * u * u + q2_bar_N * v + q3_bar * v * v +
+          double kernel_term_N =
+              -(1.0 - exp(-T_var / params.T0)) * P_star_psi[idx];
+          psiN[idx] = params.p3_bar * u * u + params.p4_bar * u * u * u +
+                      q2_bar_N * v + q3_bar * v * v +
                       params.q4_bar * v * v * v - kernel_term_N;
-          local_FE += params.p3_bar * u * u * u / 3. + params.p4_bar * u * u * u * u / 4. + q2_bar_N * u * v / 2. +
-                      q3_bar * u * v * v / 3. + params.q4_bar * u * v * v * v / 4. + -u * kernel_term_N * u / 2. +
-                      -u * P_star_psi[idx] / 2. + params.p2_bar * u * u / 2. + params.q2_bar * u * v / 2.;
+          local_FE += params.p3_bar * u * u * u / 3. +
+                      params.p4_bar * u * u * u * u / 4. +
+                      q2_bar_N * u * v / 2. + q3_bar * u * v * v / 3. +
+                      params.q4_bar * u * v * v * v / 4. +
+                      -u * kernel_term_N * u / 2. + -u * P_star_psi[idx] / 2. +
+                      params.p2_bar * u * u / 2. + params.q2_bar * u * v / 2.;
           idx++;
         }
       }
@@ -443,11 +458,10 @@ void from_json(const json &j, Aluminum &m) {
   j.at("q31_bar").get_to(p.q31_bar);
   j.at("q40_bar").get_to(p.q40_bar);
   /*
-    p.q20_bar = p.q20 + 2.0 * p.shift_s * p.q30 + 3.0 * pow(p.shift_s, 2) * p.q40;
-    p.q21_bar = p.q21 + 2.0 * p.shift_s * p.q31;
-    p.q30_bar = p.shift_u * (p.q30 + 3.0 * p.shift_s * p.q40);
-    p.q31_bar = p.shift_u * p.q31;
-    p.q40_bar = pow(p.shift_u, 2) * p.q40;
+    p.q20_bar = p.q20 + 2.0 * p.shift_s * p.q30 + 3.0 * pow(p.shift_s, 2) *
+    p.q40; p.q21_bar = p.q21 + 2.0 * p.shift_s * p.q31; p.q30_bar = p.shift_u *
+    (p.q30 + 3.0 * p.shift_s * p.q40); p.q31_bar = p.shift_u * p.q31; p.q40_bar
+    = pow(p.shift_u, 2) * p.q40;
   */
   p.q2_bar = p.q21_bar * p.tau_const + p.q20_bar;
   p.q2_bar_L = p.q2_bar;
@@ -473,7 +487,8 @@ void step(Simulator &s, Aluminum &m) {
       // auto moving = dynamic_cast< MovingBC& >(*bc);
       // double newxpos = moving.get_xpos();
       // m.set_m_xpos(newxpos);
-      // if (m.rank0) std::cout << "Updated xpos to " << m.params.m_xpos << std::endl;
+      // if (m.rank0) std::cout << "Updated xpos to " << m.params.m_xpos <<
+      // std::endl;
     }
   }
 

apps/aluminumNew/SeedFCC.hpp

@@ -98,8 +98,10 @@ class SeedFCC {
    * @return vec32
    */
   vec32 bounding_box(const vec3 &location, double radius) {
-    const vec3 low = {location[0] - radius, location[1] - radius, location[2] - radius};
-    const vec3 high = {location[0] + radius, location[1] + radius, location[2] + radius};
+    const vec3 low = {location[0] - radius, location[1] - radius,
+                      location[2] - radius};
+    const vec3 high = {location[0] + radius, location[1] + radius,
+                       location[2] + radius};
     const vec32 bbox = {low, high};
     return bbox;
   }
@@ -113,8 +115,9 @@ class SeedFCC {
    */
   inline bool is_inside_bbox(const vec3 &location) const {
     const vec32 bbox = get_bbox();
-    return (location[0] > bbox[0][0]) && (location[0] < bbox[1][0]) && (location[1] > bbox[0][1]) &&
-           (location[1] < bbox[1][1]) && (location[2] > bbox[0][2]) && (location[2] < bbox[1][2]);
+    return (location[0] > bbox[0][0]) && (location[0] < bbox[1][0]) &&
+           (location[1] > bbox[0][1]) && (location[1] < bbox[1][1]) &&
+           (location[2] > bbox[0][2]) && (location[2] < bbox[1][2]);
   }
 
   double get_radius() const { return radius_; }
@@ -134,9 +137,11 @@ class SeedFCC {
    * @param rho Density of the seed
    * @param amplitude Amplitude of the seed
    */
-  SeedFCC(const vec3 &location, const vec3 &orientation, const double radius, const double rho, const double amplitude)
-      : location_(location), orientation_(orientation), q_(rotate(orientation)), bbox_(bounding_box(location, radius)),
-        rho_(rho), radius_(radius), amplitude_(amplitude) {}
+  SeedFCC(const vec3 &location, const vec3 &orientation, const double radius,
+          const double rho, const double amplitude)
+      : location_(location), orientation_(orientation), q_(rotate(orientation)),
+        bbox_(bounding_box(location, radius)), rho_(rho), radius_(radius),
+        amplitude_(amplitude) {}
 
   /**
    * @brief Check if a point is inside the seed.

apps/aluminumNew/SeedGridFCC.hpp

@@ -15,7 +15,8 @@ using json = nlohmann::json;
 using namespace pfc;
 
 /**
- * @brief SeedGridFCC is a FieldModifier that seeds the model with a grid of FCC seeds.
+ * @brief SeedGridFCC is a FieldModifier that seeds the model with a grid of FCC
+ * seeds.
  *
  */
 class SeedGridFCC : public FieldModifier {
@@ -29,15 +30,10 @@ class SeedGridFCC : public FieldModifier {
 public:
   SeedGridFCC() = default;
 
-  SeedGridFCC(int Ny, int Nz, double X0, double radius, double amplitude, double rho, double rseed)
-      : m_Nx(1),
-        m_Ny(Ny),
-        m_Nz(Nz),
-        m_X0(X0),
-        m_radius(radius),
-        m_amplitude(amplitude),
-        m_rho(rho),
-        m_rseed(rseed) {}
+  SeedGridFCC(int Ny, int Nz, double X0, double radius, double amplitude,
+              double rho, double rseed)
+      : m_Nx(1), m_Ny(Ny), m_Nz(Nz), m_X0(X0), m_radius(radius),
+        m_amplitude(amplitude), m_rho(rho), m_rseed(rseed) {}
 
   // getters
   int get_Nx() const { return m_Nx; }
@@ -102,15 +98,17 @@ class SeedGridFCC : public FieldModifier {
     double Z0 = Dz / 2.0;
     int nseeds = Nx * Ny * Nz;
 
-    std::cout << "Generating " << nseeds << " regular seeds with radius " << radius << "\n";
+    std::cout << "Generating " << nseeds << " regular seeds with radius "
+              << radius << "\n";
 
     std::mt19937_64 re(rseed);
     std::uniform_real_distribution<double> rt(-0.2 * radius, 0.2 * radius);
     std::uniform_real_distribution<double> rr(0.0, 8.0 * atan(1.0));
 
     for (int j = 0; j < Ny; j++) {
       for (int k = 0; k < Nz; k++) {
-        const std::array<double, 3> location = {X0 + rt(re), Y0 + Dy * j + rt(re), Z0 + Dz * k + rt(re)};
+        const std::array<double, 3> location = {
+            X0 + rt(re), Y0 + Dy * j + rt(re), Z0 + Dz * k + rt(re)};
         const std::array<double, 3> orientation = {rr(re), rr(re), rr(re)};
         const SeedFCC seed(location, orientation, radius, rho, amplitude);
         seeds.push_back(seed);
@@ -150,39 +148,46 @@ class SeedGridFCC : public FieldModifier {
  * { "type": "seed_grid_fcc", "X0": 130.0, "Ny": 2, "Nz": 1, "radius": 120,
  * "amplitude": 0.4, "rho": -0.036, "rseed": 42 }
  *
- * The "type" field is required and must be "seed_grid_fcc". The "rseed" field is
- * optional and defaults to 0. All other fields are required. The "Ny" and "Nz"
- * fields are the number of seeds in the y and z directions, respectively. The
- * "X0" field is the x-coordinate of the center of the first seed. The "radius"
- * field is the radius of the seeds. The "amplitude" field is the amplitude of
- * the seed. The "rho" field is the background density. The "rseed" field is the
- * random seed.
+ * The "type" field is required and must be "seed_grid_fcc". The "rseed" field
+ * is optional and defaults to 0. All other fields are required. The "Ny" and
+ * "Nz" fields are the number of seeds in the y and z directions, respectively.
+ * The "X0" field is the x-coordinate of the center of the first seed. The
+ * "radius" field is the radius of the seeds. The "amplitude" field is the
+ * amplitude of the seed. The "rho" field is the background density. The "rseed"
+ * field is the random seed.
  *
  */
 void from_json(const json &params, SeedGridFCC &ic) {
   std::cout << "Parsing SeedGridFCC from json" << std::endl;
 
   // check for required fields
   if (!params.contains("amplitude") || !params["amplitude"].is_number()) {
-    throw std::invalid_argument("Reading SeedGridFCC failed: missing or invalid 'amplitude' field.");
+    throw std::invalid_argument(
+        "Reading SeedGridFCC failed: missing or invalid 'amplitude' field.");
   }
   if (!params.contains("radius") || !params["radius"].is_number()) {
-    throw std::invalid_argument("Reading SeedGridFCC failed: missing or invalid 'radius' field.");
+    throw std::invalid_argument(
+        "Reading SeedGridFCC failed: missing or invalid 'radius' field.");
   }
   if (!params.contains("rho") || !params["rho"].is_number()) {
-    throw std::invalid_argument("Reading SeedGridFCC failed: missing or invalid 'rho' field.");
+    throw std::invalid_argument(
+        "Reading SeedGridFCC failed: missing or invalid 'rho' field.");
   }
   if (!params.contains("Ny") || !params["Ny"].is_number()) {
-    throw std::invalid_argument("Reading SeedGridFCC failed: missing or invalid 'Ny' field.");
+    throw std::invalid_argument(
+        "Reading SeedGridFCC failed: missing or invalid 'Ny' field.");
   }
   if (!params.contains("Nz") || !params["Nz"].is_number()) {
-    throw std::invalid_argument("Reading SeedGridFCC failed: missing or invalid 'Nz' field.");
+    throw std::invalid_argument(
+        "Reading SeedGridFCC failed: missing or invalid 'Nz' field.");
   }
   if (!params.contains("X0") || !params["X0"].is_number()) {
-    throw std::invalid_argument("Reading SeedGridFCC failed: missing or invalid 'X0' field.");
+    throw std::invalid_argument(
+        "Reading SeedGridFCC failed: missing or invalid 'X0' field.");
   }
   if (!params.contains("rseed") || !params["rseed"].is_number()) {
-    std::cout << "No valid random seed detected, using default value 0." << std::endl;
+    std::cout << "No valid random seed detected, using default value 0."
+              << std::endl;
   }
 
   ic.set_Ny(params["Ny"]);
@@ -191,7 +196,8 @@ void from_json(const json &params, SeedGridFCC &ic) {
   ic.set_radius(params["radius"]);
   ic.set_amplitude(params["amplitude"]);
   ic.set_rho(params["rho"]);
-  if (params.contains("rseed") && params["rseed"].is_number()) ic.set_rseed(params["rseed"]);
+  if (params.contains("rseed") && params["rseed"].is_number())
+    ic.set_rseed(params["rseed"]);
 }
 
 #endif // SEEDGRIDFCC_HPP