Merge pull request #1389 from Iximiel/feature/scalaeAtomDistribution

Author: carlocamilloni

CHANGES/v2.11.md

@@ -5,10 +5,12 @@ This page contains changes that will end up in 2.11
 ### Changes relevant for users:
 
   - When using [MOLINFO](MOLINFO.md) with the `WHOLE` flag, PBCs in the following actions will be reconstructed using a minimum spanning tree based on the coordinates stored in the MOLFILE reference pdb.
+  - When using the benchmark now it is possible to scale the atom distances in the synthetic atom distribution (the base atomic distance is 1)
 
 ### Changes relevant for developers:
 
   - The inputlines now are parsed using a dictionary instead of an array. This speeds up the parsing of massive input lines.
+  - Abstracted the AtomDistribution functionality from the benchmark. It can be used in tests or in other
   - It is not possible anymore to register lowercase keywords and the developer must always specify the keywords completely as uppercase while parsing in the action constructor. There are no differences for the user, apart the entry in the manual for the DEBUG action: the user can still specify lowercase and mixed case keywords in the input file.
   - Some improvements in the management of the plugins:
     - Now the plugins have a common directory structure

regtest/tools/rt-make-AtomicDistribution/main.cpp

@@ -35,6 +35,7 @@ void atomsInBoxCheck(
     ofs <<header <<" all atoms in box along " <<xyz[j]<<" : "<< (upbound[j]<box[j*3+j]) << "\n";
   }
 }
+
 void basecheck(std::string_view kind, std::ostream & ofs) {
   std::string header= "[baseCheck -"+ std::string(kind) + "-]:";
   ofs << header << "\n";
@@ -61,25 +62,49 @@ void replyTrajCheck(std::string_view kind,
   std::vector<double> basebox(9);
   unsigned nat = atoms.size();
   const auto oldNat=nat;
-  auto rep= std::make_unique<repliedTrajectory>([&]() {
+
+  std::unique_ptr<PLMD::AtomDistribution> rep= std::make_unique<repliedTrajectory>([&]() {
     auto d = AtomDistribution::getAtomDistribution(kind);
     d->frame(atoms,basebox,0,rng);
     return d;
   }
   (),
-  num[0],
-  num[1],
-  num[2],
+  num[0], num[1], num[2],
   nat);
 
   //this must return true
   ofs <<header<< " rep->overrideNat(nat)=" <<
       rep->overrideNat(nat) <<"\n";
-  ofs <<header<< " new number of atoms: ( should be " << oldNat*num[0]*num[1]*num[2] << ") : " << nat <<"\n";
+  ofs << header << " new number of atoms: ( should be " << oldNat*num[0]*num[1]*num[2] << ") : " << nat <<"\n";
   atoms.resize(nat);
   std::vector<double> box(9);
-  rep->frame(atoms,box,0,rng);
+  //the next frame is generated exactly as the "base one"
+  //so that we can use the same base configuration
+  Random rng2;
+  rng2.setSeed(12345);
+  rep->frame(atoms,box,0,rng2);
 
+  ofs << header << "The atoms are replicated correctly:\t";
+  bool correct = true;
+  Vector boxX(basebox[0],basebox[1],basebox[2]);
+  Vector boxY(basebox[3],basebox[4],basebox[5]);
+  Vector boxZ(basebox[6],basebox[7],basebox[8]);
+  unsigned j=0;
+  for (unsigned x=0; x<num[0] && correct; ++x) {
+    for (unsigned y=0; y<num[1] && correct; ++y) {
+      for (unsigned z=0; z<num[2] && correct; ++z) {
+        for (unsigned i=0; i<oldNat && correct; ++i) {
+          auto tmp = atoms[i] + (x * boxX + y * boxY + z * boxZ);
+          correct = (abs(tmp[0] - atoms[j][0]) < 1000*PLMD::epsilon)&&
+                    (abs(tmp[1] - atoms[j][1]) < 1000*PLMD::epsilon)&&
+                    (abs(tmp[2] - atoms[j][2]) < 1000*PLMD::epsilon);
+          ++j;
+        }
+      }
+    }
+  }
+
+  ofs << correct << "\n";
   atomsInBoxCheck(atoms,box,header,ofs);
   ofs << "New box has the correct dimensions:\n";
   for (unsigned j=0; j<3; ++j) {
@@ -88,6 +113,58 @@ void replyTrajCheck(std::string_view kind,
   }
 }
 
+void scaleTrajCheck(std::string_view kind,
+                    const double scale,
+                    std::ostream & ofs) {
+  std::stringstream ss;
+  ss << "[scaleTrajCheck -" << kind << "*"<< scale << "-]:";
+  auto header = ss.str();
+  ofs << header << "\n";
+  //reinitialized each time for stability
+  Random rng;
+  rng.setSeed(12345);
+  std::vector<Vector> baseatoms(200);
+  std::vector<double> basebox(9);
+  std::unique_ptr<PLMD::AtomDistribution> scaled= std::make_unique<scaledTrajectory>([&]() {
+    std::unique_ptr<PLMD::AtomDistribution> d;
+    if (kind == "sphere-reply212") {
+      d = std::make_unique<repliedTrajectory>(
+            AtomDistribution::getAtomDistribution("sphere"),
+            2,1,2,baseatoms.size()/(2*1*2));
+    } else {
+      d = AtomDistribution::getAtomDistribution(kind);
+    }
+    d->frame(baseatoms,basebox,0,rng);
+    return d;
+  }
+  (),
+  scale);
+
+  std::vector<Vector> atoms(200);
+  std::vector<double> box(9);
+  //the next frame is generated exactly as the "base one"
+  //so that we can use the same base configuration
+  Random rng2;
+  rng2.setSeed(12345);
+  scaled->frame(atoms,box,0,rng2);
+
+  ofs << header << "The atoms are scaled correctly:\t";
+  bool correct = true;
+  for(unsigned i =0; i< atoms.size() && correct; ++i) {
+    correct = (abs(scale*baseatoms[i][0] - atoms[i][0]) < 1000*PLMD::epsilon)&&
+              (abs(scale*baseatoms[i][1] - atoms[i][1]) < 1000*PLMD::epsilon)&&
+              (abs(scale*baseatoms[i][2] - atoms[i][2]) < 1000*PLMD::epsilon);
+
+  }
+  ofs << correct << "\n";
+
+  atomsInBoxCheck(atoms,box,header,ofs);
+  ofs << "New box has the correct dimensions:\n";
+  for (unsigned j=0; j<3; ++j) {
+    ofs <<header <<" correct box dimension " <<xyz[j]<<" : "
+        << ((scale*basebox[j*3+j] - box[j*3+j]) < 1000*PLMD::epsilon) << "\n";
+  }
+}
 
 int main() {
   std::ofstream ofs("output");
@@ -110,5 +187,14 @@ int main() {
     replyTrajCheck("sphere",num,ofs);
     ofs << "\n";
   }
+  for (auto num : {
+         0.5, 3.0, 10.0
+       }) {
+    scaleTrajCheck("sphere",num,ofs);
+    scaleTrajCheck("sc",num,ofs);
+    scaleTrajCheck("globs",num,ofs);
+    scaleTrajCheck("sphere-reply212",num,ofs);
+    ofs << "\n";
+  }
   return 0;
 }

regtest/tools/rt-make-AtomicDistribution/output.reference

@@ -31,6 +31,7 @@ Atoms are within box dimensions:
 [replyTrajCheck -sphere 1, 2, 3-]:
 [replyTrajCheck -sphere 1, 2, 3-]: rep->overrideNat(nat)=true
 [replyTrajCheck -sphere 1, 2, 3-]: new number of atoms: ( should be 1200) : 1200
+[replyTrajCheck -sphere 1, 2, 3-]:The atoms are replicated correctly:	true
 Atoms are within box dimensions:
 [replyTrajCheck -sphere 1, 2, 3-]: all atoms in box along x : true
 [replyTrajCheck -sphere 1, 2, 3-]: all atoms in box along y : true
@@ -43,6 +44,7 @@ New box has the correct dimensions:
 [replyTrajCheck -sphere 2, 2, 2-]:
 [replyTrajCheck -sphere 2, 2, 2-]: rep->overrideNat(nat)=true
 [replyTrajCheck -sphere 2, 2, 2-]: new number of atoms: ( should be 1600) : 1600
+[replyTrajCheck -sphere 2, 2, 2-]:The atoms are replicated correctly:	true
 Atoms are within box dimensions:
 [replyTrajCheck -sphere 2, 2, 2-]: all atoms in box along x : true
 [replyTrajCheck -sphere 2, 2, 2-]: all atoms in box along y : true
@@ -55,6 +57,7 @@ New box has the correct dimensions:
 [replyTrajCheck -sphere 1, 1, 1-]:
 [replyTrajCheck -sphere 1, 1, 1-]: rep->overrideNat(nat)=true
 [replyTrajCheck -sphere 1, 1, 1-]: new number of atoms: ( should be 200) : 200
+[replyTrajCheck -sphere 1, 1, 1-]:The atoms are replicated correctly:	true
 Atoms are within box dimensions:
 [replyTrajCheck -sphere 1, 1, 1-]: all atoms in box along x : true
 [replyTrajCheck -sphere 1, 1, 1-]: all atoms in box along y : true
@@ -67,6 +70,7 @@ New box has the correct dimensions:
 [replyTrajCheck -sphere 3, 2, 1-]:
 [replyTrajCheck -sphere 3, 2, 1-]: rep->overrideNat(nat)=true
 [replyTrajCheck -sphere 3, 2, 1-]: new number of atoms: ( should be 1200) : 1200
+[replyTrajCheck -sphere 3, 2, 1-]:The atoms are replicated correctly:	true
 Atoms are within box dimensions:
 [replyTrajCheck -sphere 3, 2, 1-]: all atoms in box along x : true
 [replyTrajCheck -sphere 3, 2, 1-]: all atoms in box along y : true
@@ -79,6 +83,7 @@ New box has the correct dimensions:
 [replyTrajCheck -sphere 3, 4, 7-]:
 [replyTrajCheck -sphere 3, 4, 7-]: rep->overrideNat(nat)=true
 [replyTrajCheck -sphere 3, 4, 7-]: new number of atoms: ( should be 16800) : 16800
+[replyTrajCheck -sphere 3, 4, 7-]:The atoms are replicated correctly:	true
 Atoms are within box dimensions:
 [replyTrajCheck -sphere 3, 4, 7-]: all atoms in box along x : true
 [replyTrajCheck -sphere 3, 4, 7-]: all atoms in box along y : true
@@ -91,6 +96,7 @@ New box has the correct dimensions:
 [replyTrajCheck -sphere 5, 1, 1-]:
 [replyTrajCheck -sphere 5, 1, 1-]: rep->overrideNat(nat)=true
 [replyTrajCheck -sphere 5, 1, 1-]: new number of atoms: ( should be 1000) : 1000
+[replyTrajCheck -sphere 5, 1, 1-]:The atoms are replicated correctly:	true
 Atoms are within box dimensions:
 [replyTrajCheck -sphere 5, 1, 1-]: all atoms in box along x : true
 [replyTrajCheck -sphere 5, 1, 1-]: all atoms in box along y : true
@@ -103,6 +109,7 @@ New box has the correct dimensions:
 [replyTrajCheck -sphere 1, 3, 1-]:
 [replyTrajCheck -sphere 1, 3, 1-]: rep->overrideNat(nat)=true
 [replyTrajCheck -sphere 1, 3, 1-]: new number of atoms: ( should be 600) : 600
+[replyTrajCheck -sphere 1, 3, 1-]:The atoms are replicated correctly:	true
 Atoms are within box dimensions:
 [replyTrajCheck -sphere 1, 3, 1-]: all atoms in box along x : true
 [replyTrajCheck -sphere 1, 3, 1-]: all atoms in box along y : true
@@ -115,6 +122,7 @@ New box has the correct dimensions:
 [replyTrajCheck -sphere 1, 1, 7-]:
 [replyTrajCheck -sphere 1, 1, 7-]: rep->overrideNat(nat)=true
 [replyTrajCheck -sphere 1, 1, 7-]: new number of atoms: ( should be 1400) : 1400
+[replyTrajCheck -sphere 1, 1, 7-]:The atoms are replicated correctly:	true
 Atoms are within box dimensions:
 [replyTrajCheck -sphere 1, 1, 7-]: all atoms in box along x : true
 [replyTrajCheck -sphere 1, 1, 7-]: all atoms in box along y : true
@@ -124,3 +132,126 @@ New box has the correct dimensions:
 [replyTrajCheck -sphere 1, 1, 7-]: correct box dimension y : true
 [replyTrajCheck -sphere 1, 1, 7-]: correct box dimension z : true
 
+[scaleTrajCheck -sphere*0.5-]:
+[scaleTrajCheck -sphere*0.5-]:The atoms are scaled correctly:	true
+Atoms are within box dimensions:
+[scaleTrajCheck -sphere*0.5-]: all atoms in box along x : true
+[scaleTrajCheck -sphere*0.5-]: all atoms in box along y : true
+[scaleTrajCheck -sphere*0.5-]: all atoms in box along z : true
+New box has the correct dimensions:
+[scaleTrajCheck -sphere*0.5-]: correct box dimension x : true
+[scaleTrajCheck -sphere*0.5-]: correct box dimension y : true
+[scaleTrajCheck -sphere*0.5-]: correct box dimension z : true
+[scaleTrajCheck -sc*0.5-]:
+[scaleTrajCheck -sc*0.5-]:The atoms are scaled correctly:	true
+Atoms are within box dimensions:
+[scaleTrajCheck -sc*0.5-]: all atoms in box along x : true
+[scaleTrajCheck -sc*0.5-]: all atoms in box along y : true
+[scaleTrajCheck -sc*0.5-]: all atoms in box along z : true
+New box has the correct dimensions:
+[scaleTrajCheck -sc*0.5-]: correct box dimension x : true
+[scaleTrajCheck -sc*0.5-]: correct box dimension y : true
+[scaleTrajCheck -sc*0.5-]: correct box dimension z : true
+[scaleTrajCheck -globs*0.5-]:
+[scaleTrajCheck -globs*0.5-]:The atoms are scaled correctly:	true
+Atoms are within box dimensions:
+[scaleTrajCheck -globs*0.5-]: all atoms in box along x : true
+[scaleTrajCheck -globs*0.5-]: all atoms in box along y : true
+[scaleTrajCheck -globs*0.5-]: all atoms in box along z : true
+New box has the correct dimensions:
+[scaleTrajCheck -globs*0.5-]: correct box dimension x : true
+[scaleTrajCheck -globs*0.5-]: correct box dimension y : true
+[scaleTrajCheck -globs*0.5-]: correct box dimension z : true
+[scaleTrajCheck -sphere-reply212*0.5-]:
+[scaleTrajCheck -sphere-reply212*0.5-]:The atoms are scaled correctly:	true
+Atoms are within box dimensions:
+[scaleTrajCheck -sphere-reply212*0.5-]: all atoms in box along x : true
+[scaleTrajCheck -sphere-reply212*0.5-]: all atoms in box along y : true
+[scaleTrajCheck -sphere-reply212*0.5-]: all atoms in box along z : true
+New box has the correct dimensions:
+[scaleTrajCheck -sphere-reply212*0.5-]: correct box dimension x : true
+[scaleTrajCheck -sphere-reply212*0.5-]: correct box dimension y : true
+[scaleTrajCheck -sphere-reply212*0.5-]: correct box dimension z : true
+
+[scaleTrajCheck -sphere*3-]:
+[scaleTrajCheck -sphere*3-]:The atoms are scaled correctly:	true
+Atoms are within box dimensions:
+[scaleTrajCheck -sphere*3-]: all atoms in box along x : true
+[scaleTrajCheck -sphere*3-]: all atoms in box along y : true
+[scaleTrajCheck -sphere*3-]: all atoms in box along z : true
+New box has the correct dimensions:
+[scaleTrajCheck -sphere*3-]: correct box dimension x : true
+[scaleTrajCheck -sphere*3-]: correct box dimension y : true
+[scaleTrajCheck -sphere*3-]: correct box dimension z : true
+[scaleTrajCheck -sc*3-]:
+[scaleTrajCheck -sc*3-]:The atoms are scaled correctly:	true
+Atoms are within box dimensions:
+[scaleTrajCheck -sc*3-]: all atoms in box along x : true
+[scaleTrajCheck -sc*3-]: all atoms in box along y : true
+[scaleTrajCheck -sc*3-]: all atoms in box along z : true
+New box has the correct dimensions:
+[scaleTrajCheck -sc*3-]: correct box dimension x : true
+[scaleTrajCheck -sc*3-]: correct box dimension y : true
+[scaleTrajCheck -sc*3-]: correct box dimension z : true
+[scaleTrajCheck -globs*3-]:
+[scaleTrajCheck -globs*3-]:The atoms are scaled correctly:	true
+Atoms are within box dimensions:
+[scaleTrajCheck -globs*3-]: all atoms in box along x : true
+[scaleTrajCheck -globs*3-]: all atoms in box along y : true
+[scaleTrajCheck -globs*3-]: all atoms in box along z : true
+New box has the correct dimensions:
+[scaleTrajCheck -globs*3-]: correct box dimension x : true
+[scaleTrajCheck -globs*3-]: correct box dimension y : true
+[scaleTrajCheck -globs*3-]: correct box dimension z : true
+[scaleTrajCheck -sphere-reply212*3-]:
+[scaleTrajCheck -sphere-reply212*3-]:The atoms are scaled correctly:	true
+Atoms are within box dimensions:
+[scaleTrajCheck -sphere-reply212*3-]: all atoms in box along x : true
+[scaleTrajCheck -sphere-reply212*3-]: all atoms in box along y : true
+[scaleTrajCheck -sphere-reply212*3-]: all atoms in box along z : true
+New box has the correct dimensions:
+[scaleTrajCheck -sphere-reply212*3-]: correct box dimension x : true
+[scaleTrajCheck -sphere-reply212*3-]: correct box dimension y : true
+[scaleTrajCheck -sphere-reply212*3-]: correct box dimension z : true
+
+[scaleTrajCheck -sphere*10-]:
+[scaleTrajCheck -sphere*10-]:The atoms are scaled correctly:	true
+Atoms are within box dimensions:
+[scaleTrajCheck -sphere*10-]: all atoms in box along x : true
+[scaleTrajCheck -sphere*10-]: all atoms in box along y : true
+[scaleTrajCheck -sphere*10-]: all atoms in box along z : true
+New box has the correct dimensions:
+[scaleTrajCheck -sphere*10-]: correct box dimension x : true
+[scaleTrajCheck -sphere*10-]: correct box dimension y : true
+[scaleTrajCheck -sphere*10-]: correct box dimension z : true
+[scaleTrajCheck -sc*10-]:
+[scaleTrajCheck -sc*10-]:The atoms are scaled correctly:	true
+Atoms are within box dimensions:
+[scaleTrajCheck -sc*10-]: all atoms in box along x : true
+[scaleTrajCheck -sc*10-]: all atoms in box along y : true
+[scaleTrajCheck -sc*10-]: all atoms in box along z : true
+New box has the correct dimensions:
+[scaleTrajCheck -sc*10-]: correct box dimension x : true
+[scaleTrajCheck -sc*10-]: correct box dimension y : true
+[scaleTrajCheck -sc*10-]: correct box dimension z : true
+[scaleTrajCheck -globs*10-]:
+[scaleTrajCheck -globs*10-]:The atoms are scaled correctly:	true
+Atoms are within box dimensions:
+[scaleTrajCheck -globs*10-]: all atoms in box along x : true
+[scaleTrajCheck -globs*10-]: all atoms in box along y : true
+[scaleTrajCheck -globs*10-]: all atoms in box along z : true
+New box has the correct dimensions:
+[scaleTrajCheck -globs*10-]: correct box dimension x : true
+[scaleTrajCheck -globs*10-]: correct box dimension y : true
+[scaleTrajCheck -globs*10-]: correct box dimension z : true
+[scaleTrajCheck -sphere-reply212*10-]:
+[scaleTrajCheck -sphere-reply212*10-]:The atoms are scaled correctly:	true
+Atoms are within box dimensions:
+[scaleTrajCheck -sphere-reply212*10-]: all atoms in box along x : true
+[scaleTrajCheck -sphere-reply212*10-]: all atoms in box along y : true
+[scaleTrajCheck -sphere-reply212*10-]: all atoms in box along z : true
+New box has the correct dimensions:
+[scaleTrajCheck -sphere-reply212*10-]: correct box dimension x : true
+[scaleTrajCheck -sphere-reply212*10-]: correct box dimension y : true
+[scaleTrajCheck -sphere-reply212*10-]: correct box dimension z : true
+

regtest/tools/rt-make-CellLists/main.cpp

@@ -21,6 +21,7 @@
 #include <numeric>
 
 using namespace PLMD;
+using atomDst = std::unique_ptr<PLMD::AtomDistribution>;
 
 void test (PLMD::Communicator &comm);
 void testIndexes (PLMD::Communicator &comm);
@@ -363,7 +364,7 @@ void test (PLMD::Communicator &comm) {
   std::vector<Vector> atoms(5*5*5);
   std::vector<double> basebox(9);
   unsigned nat = atoms.size();
-  auto rep= std::make_unique<repliedTrajectory>([&]() {
+  atomDst rep= std::make_unique<repliedTrajectory>([&]() {
     auto d = AtomDistribution::getAtomDistribution("sc");
 //getting some base informations
     d->frame(atoms,basebox,0,rng);
@@ -433,7 +434,7 @@ void bench (PLMD::Communicator &comm) {
   std::vector<Vector> atoms(50000);
   std::vector<double> basebox(9);
   unsigned nat = atoms.size();
-  auto rep= std::make_unique<repliedTrajectory>([&]() {
+  atomDst rep= std::make_unique<repliedTrajectory>([&]() {
     auto d = AtomDistribution::getAtomDistribution("cube");
 //getting some base informations
     d->frame(atoms,basebox,0,rng);