diff --git a/test_build.sh b/checks/check-buildOptions_mixed.sh
similarity index 100%
rename from test_build.sh
rename to checks/check-buildOptions_mixed.sh
diff --git a/checks/check-buildOptions.sh b/checks/check-buildOptions_single.sh
similarity index 100%
rename from checks/check-buildOptions.sh
rename to checks/check-buildOptions_single.sh
diff --git a/examples/argon.sh b/examples/argon.sh
deleted file mode 100755
index 19a57dd935..0000000000
--- a/examples/argon.sh
+++ /dev/null
@@ -1,55 +0,0 @@
-#!/bin/bash
-# Testscript running Argon Example
-#
-# Copyright (c) 2018 Moritz Kruegener
-#
-
-MARDYN_EXE="mpirun -np 1 $PWD/../src/MarDyn"
-MARDYN_OPTIONS="--steps 10 -v"
-LOGFILE=${LOGFILE:=$PWD/argon.log}
-
-all_examples="./Argon/200K_18mol_l/config.xml"
-#while IFS= read -r; do all_examples+=("$REPLY"); done < $EXAMPLE_LIST_FILE
-
-failed_examples=()
-
-# definitions for easier color output to display
-Color_Off='\e[0m' # Text Reset
-IGreen='\e[0;92m' # Intense Green
-IRed='\e[0;91m' # Intense Red
-IMagenta='\e[0;95m' # magenta
-
-logfile=$LOGFILE
-date > $logfile
-for example in ${all_examples[@]}
-do
- example_dir=$(dirname $example)
- example_inp_file=$(basename $example)
- echo -e -n "Running example ${IMagenta}$example_inp_file${Color_Off} in $example_dir ... "
- echo "Running example $example_inp_file in $example_dir" >> $logfile
- pushd "$example_dir" >/dev/null
- cmd="$MARDYN_EXE $MARDYN_OPTIONS $example_inp_file"
- echo $cmd >>$logfile
- { $cmd ; } 2>&1 | tee $logfile
- ret=$?
- if [ $ret -eq 0 ]; then
- echo -e "${IGreen}success${Color_Off}"
- echo "Running example $example_inp_file in $example_dir ... Result: success" >> $logfile
- else
- failed_examples=(${failed_examples[@]} $example)
- echo -e "${IRed}failed${Color_Off}"
- echo "Running example $example_inp_file in $example_dir ... Result: failed" >> $logfile
- fi
- popd >/dev/null
-done
-
-echo "----------------------------------------"
-echo "Summary of tested examples:"
-echo "----------------------------------------"
-echo "num tested examples: ${#all_examples[@]}"
-echo "num failed examples: ${#failed_examples[@]}"
-echo "----------------------------------------"
-
-date >> $logfile
-exit ${#failed_examples[@]}
-
diff --git a/examples/comparison.xml b/examples/comparison.xml
deleted file mode 100644
index 1a4fbaccd4..0000000000
--- a/examples/comparison.xml
+++ /dev/null
@@ -1,99 +0,0 @@
-
-
-
- 0.0529177
- 1000
- 27.2126
-
-
-
- 0.0005
-
-
- 0
-
- 100000
-
-
-
- 0.86232
-
- 72.7626
- 62.9432
- 72.7626
-
-
-
-
- 0.0 0.0 0.0
- 1.0
- 1.0
- 1.0
- false
-
-
- 0.0
- 0.0
- 0.0
-
-
-
-
- Ads_LJ1043.inp
-
-
-
-
-
- 1
-
-
-
- 2.5
-
-
-
- 1.0e+10
-
-
-
-
-
-
- 0.86232
-
-
-
-
-
-
-
-
- 104
- 1.07
-
- 100
- 1
- 4.75
- 51
- 0.775
-
- 0.0514
- 1
-
-
-
-
- 55
- 20
- 0
-
-
-
-
diff --git a/src/bhfmm/fft/doc/Rescaling.txt b/src/bhfmm/fft/doc/Rescaling.txt
deleted file mode 100644
index e69de29bb2..0000000000
diff --git a/tools/Makefile b/tools/Makefile
deleted file mode 100644
index 97ad63c8ea..0000000000
--- a/tools/Makefile
+++ /dev/null
@@ -1,26 +0,0 @@
-MACHTYPE = SEQ
-TARGET = RELEASE
-
-INCLUDES = -I$(shell pwd)
-
-include ../makefile/cfg/gcc.in
-
-CXX = $(CXX_$(MACHTYPE))
-CXXFLAGS = $(CXXFLAGS_$(MACHTYPE)_$(TARGET))
-LINKFLAGS = $(LINKFLAGS_$(MACHTYPE)_$(TARGET))
-
-OBJECTS_TINYXPATH = $(patsubst %.cpp,%.o,$(shell find ../src/External/tinyxpath -name '*.cpp'))
-
-all: moldy2mardyn mdproject2mardyn
-
-moldy2mardyn: moldy2mardyn.o $(OBJECTS_TINYXPATH)
- $(CXX) $(LINKFLAGS) -o moldy2mardyn moldy2mardyn.o $(OBJECTS_TINYXPATH)
-mdproject2mardyn: mdproject2mardyn.o $(OBJECTS_TINYXPATH)
- $(CXX) $(LINKFLAGS) -o mdproject2mardyn mdproject2mardyn.o $(OBJECTS_TINYXPATH)
-
-%.o: %.cpp
- $(CXX_SEQ) $(CXXFLAGS) -c $< -o $@
-
-clean:
- find -name '*.o' -exec rm -f {} \;
- rm -f mdproject2mardyn moldy2mardyn
diff --git a/tools/accumulate.cpp b/tools/accumulate.cpp
deleted file mode 100644
index 3f05788875..0000000000
--- a/tools/accumulate.cpp
+++ /dev/null
@@ -1,58 +0,0 @@
-
-#include "utils/Accumulator.h"
-#include
-#include
-#include
-#include
-
-
-/**
- * This tool computes accumulated and averaged values for pressure and potential
- * energy, from Mardyn result files.
- */
-int main(int argc, char** argsv) {
-
- if (argc != 3) {
- std::cout << "Usage: ./accumulate FILENAME NTIMES" << std::endl;
- return -1;
- }
-
- int numSteps = atoi(argsv[2]);
- std::cout << " Using file " << argsv[1] <<", averaging last " << numSteps << " steps." << std::endl;
-
- std::ifstream inputfilestream(argsv[1]);
- if (!inputfilestream.is_open()) {
- std::cerr << "Could not open file " << argsv[1] << std::endl;
- exit(1);
- }
-
- Accumulator upot_acc(numSteps);
- Accumulator p_acc(numSteps);
-
- std::string line;
- while(inputfilestream) {
- line.clear();
- getline(inputfilestream, line);
-
- if (line.empty() || line[0] == '#') {
- std::cout << " skippiing: " << line << std::endl;
- continue;
- }
-
- std::stringstream lineStream(line);
- double upot = 0;
- double p = 0;
- double dummy = 0;
-
- lineStream >> dummy >> dummy; // ignore '#step' and 't'
- lineStream >> upot;
- lineStream >> dummy; // ignore 'p_avg'
- lineStream >> p;
- upot_acc.addEntry(upot);
- p_acc.addEntry(p);
- }
-
- std::cout << "================== UPot = " << upot_acc.getAverage() << ", p = " << p_acc.getAverage() << std::endl;
- return 0;
-}
-
diff --git a/tools/grideval/Domain.cpp b/tools/grideval/Domain.cpp
deleted file mode 100644
index 83efd3c041..0000000000
--- a/tools/grideval/Domain.cpp
+++ /dev/null
@@ -1,209 +0,0 @@
-#include "Domain.h"
-
-#include
-#include
-#include
-
-Domain::Domain(int ingrid)
-{
- this->grid = ingrid;
- this->cavities = std::set();
- this->verlet = std::map< long, std::set >();
- this->clusterID = std::map();
- this->clusterVertices = std::map< long, std::set >();
-}
-
-long Domain::encode(int xgrid, int ygrid, int zgrid)
-{
- if((xgrid < 0) || (ygrid < 0) || (zgrid < 0) || (xgrid >= grid) || (ygrid >= grid) || (zgrid >= grid)) exit(21);
-
- return xgrid*grid*grid + ygrid*grid + zgrid;
-}
-
-void Domain::decode(int* qgrid, long code)
-{
- long rest;
- if((code < 0) || (code >= grid*grid*grid)) { std::cout << "invalid code " << code << ".\n"; exit(22); }
-
- rest = code % grid;
- qgrid[2] = rest;
- code = (code - rest) / grid;
- rest = code % grid;
- qgrid[1] = rest;
- code = (code - rest) / grid;
- rest = code % grid;
- qgrid[0] = rest;
-
- return;
-}
-
-bool Domain::neighbours(long code, std::set* vicinity)
-{
- // std::cout << "\t{";
- vicinity->clear();
- if(this->cavities.count(code) > 0)
- {
- // std::cout << code;
- int x[3];
- this->decode(x, code);
- // std::cout << " ; (" << x[0] << "/" << x[1] << "/" << x[2] << ")";
-
- int c[3];
- int y[3];
- long ycode;
- for(c[0] = -1; 1 >= c[0]; c[0]++)
- {
- for(c[1] = -1; 1 >= c[1]; c[1]++)
- {
- for(c[2] = -1; 1 >= c[2]; c[2]++)
- {
- if((c[0] == 0) || (c[1] == 0) || (c[2] == 0))
- {
- for(int d = 0; d < 3; d++)
- {
- y[d] = (x[d] + c[d]);
- if(y[d] < 0) y[d] += grid;
- else if(y[d] >= grid) y[d] -= grid;
- }
- // std::cout << " -?-> (" << y[0] << "/" << y[1] << "/" << y[2] << ")";
- ycode = this->encode(y[0], y[1], y[2]);
- if(this->cavities.count(ycode) > 0) vicinity->insert(ycode);
- }
- }
- }
- }
- }
- // std::cout << "}";
- return !vicinity->empty();
-}
-
-void Domain::build_verlet()
-{
- std::set::iterator cavit;
- for(cavit = this->cavities.begin(); cavit != this->cavities.end(); cavit++)
- {
- this->verlet[*cavit] = std::set();
- this->neighbours(*cavit, &(this->verlet[*cavit]));
- }
-}
-
-void Domain::detectClusters()
-{
- std::set::iterator acti, actj;
-
- long lowlink, tnode;
- std::set processed_nodes;
- std::set present_nodes;
- std::set unprocessed_nodes;
-
- std::stack dfs_stack;
- std::map::iterator> edgeit;
-
- for(acti = this->cavities.begin(); acti != this->cavities.end(); acti++)
- {
- // std::cout << "\t{" << *acti << "}";
- this->attach(*acti, *acti, false);
- unprocessed_nodes.insert(*acti);
- }
-
- // std::cout << "\nBuilding Verlet list:";
- this->build_verlet();
- // std::cout << " done.\n";
-
- while(!unprocessed_nodes.empty())
- {
- present_nodes.clear();
- dfs_stack.push( *(unprocessed_nodes.begin()) );
- lowlink = dfs_stack.top();
-
- while(!dfs_stack.empty())
- {
- tnode = dfs_stack.top();
- if(unprocessed_nodes.count(tnode) > 0)
- {
- if(this->clusterID[tnode] < lowlink)
- {
- lowlink = this->clusterID[tnode];
- }
- unprocessed_nodes.erase(tnode);
- present_nodes.insert(tnode);
- edgeit[tnode] = this->verlet[tnode].begin();
- }
-
- while((edgeit[tnode] != this->verlet[tnode].end()) && (unprocessed_nodes.count(*edgeit[tnode]) == 0))
- {
- edgeit[tnode] ++;
- }
- if(edgeit[tnode] != this->verlet[tnode].end())
- {
- tnode = *edgeit[tnode];
- dfs_stack.push(tnode);
- }
- else
- {
- dfs_stack.pop();
- }
- }
- for(acti = present_nodes.begin(); acti != present_nodes.end(); acti++)
- {
- processed_nodes.insert(*acti);
- attach(*acti, lowlink, true);
- }
- }
-}
-
-void Domain::attach(long vertex, long cluster, bool detach_previous)
-{
- if(cluster > vertex)
- {
- std::cout << "\nCavity " << vertex << " cannot be attached to cluster " << cluster << ".\n";
- exit(23);
- }
-
- if(detach_previous && (clusterID.count(vertex) > 0))
- {
- if(clusterVertices.count(clusterID[vertex]) > 0)
- {
- this->clusterVertices[clusterID[vertex]].erase(vertex);
- if(this->clusterVertices[clusterID[vertex]].empty())
- {
- this->clusterVertices.erase(clusterID[vertex]);
- }
- }
- }
-
- this->clusterID[vertex] = cluster;
- if(this->clusterVertices.count(cluster) == 0)
- {
- this->clusterVertices[cluster] = std::set();
- }
- this->clusterVertices[cluster].insert(vertex);
-}
-
-unsigned Domain::countClusters(std::map* thresholds)
-{
- std::map exactPopulation;
- std::map< long, std::set >::iterator cluvit;
- for(cluvit = this->clusterVertices.begin(); cluvit != this->clusterVertices.end(); cluvit++)
- {
- unsigned cavsize = cluvit->second.size();
- if(exactPopulation.count(cavsize) == 0) exactPopulation[cavsize] = 1;
- else exactPopulation[cavsize] ++;
- }
-
- unsigned largest = 0;
- std::map::iterator threshit, popit;
- for(threshit = thresholds->begin(); threshit != thresholds->end(); *threshit++)
- {
- (*thresholds)[threshit->first] = 0;
- }
- for(popit = exactPopulation.begin(); popit != exactPopulation.end(); popit++)
- {
- if(popit->first > largest) largest = popit->first;
- for(threshit = thresholds->begin(); threshit != thresholds->end(); *threshit++)
- {
- if(popit->first >= threshit->first) (*thresholds)[threshit->first] += popit->second;
- }
- }
- return largest;
-}
diff --git a/tools/grideval/Domain.h b/tools/grideval/Domain.h
deleted file mode 100644
index ed2e09a399..0000000000
--- a/tools/grideval/Domain.h
+++ /dev/null
@@ -1,37 +0,0 @@
-#ifndef DOMAIN_H
-#define DOMAIN_H
-
-#include